Header list of 1kx7.pdb file
Complete list - b 23 2 Bytes
HEADER OXYGEN STORAGE/TRANSPORT 31-JAN-02 1KX7
TITLE FAMILY OF 30 CONFORMERS OF A MONO-HEME FERROCYTOCHROME C FROM
TITLE 2 SHEWANELLA PUTREFACIENS SOLVED BY NMR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MONO-HEME C-TYPE CYTOCHROME SCYA;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: MONO-HEME FERROCYTOCHROME C;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA PUTREFACIENS;
SOURCE 3 ORGANISM_TAXID: 24;
SOURCE 4 GENE: SCYA;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)C41;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPB10SCYA
KEYWDS HAEM PROTEIN, FERROCYTOCHROME, ELECTRON TRANSPORT, GRAM NEGATIVE,
KEYWDS 2 BACTERIA, SCYA SHEWANELLA PUTREFACIENS, MONO HAEM, ALL-ALPHA, OXYGEN
KEYWDS 3 STORAGE-TRANSPORT COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 30
AUTHOR I.BARTALESI,I.BERTINI,P.HAJIEVA,A.ROSATO,P.R.VASOS
REVDAT 4 23-FEB-22 1KX7 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 1KX7 1 VERSN
REVDAT 2 19-JUN-02 1KX7 1 JRNL
REVDAT 1 13-FEB-02 1KX7 0
JRNL AUTH I.BARTALESI,I.BERTINI,P.HAJIEVA,A.ROSATO,P.R.VASOS
JRNL TITL SOLUTION STRUCTURE OF A MONOHEME FERROCYTOCHROME C FROM
JRNL TITL 2 SHEWANELLA PUTREFACIENS AND STRUCTURAL ANALYSIS OF
JRNL TITL 3 SEQUENCE-SIMILAR PROTEINS: FUNCTIONAL IMPLICATIONS.
JRNL REF BIOCHEMISTRY V. 41 5112 2002
JRNL REFN ISSN 0006-2960
JRNL PMID 11955059
JRNL DOI 10.1021/BI015984Z
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 1.5, AMBER 6
REMARK 3 AUTHORS : GUNTERT, P., MUMENTHALER, C., WUTHRICH, K.
REMARK 3 (DYANA), CASE (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1KX7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-02.
REMARK 100 THE DEPOSITION ID IS D_1000015433.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.5 MM CYTOCHROME C: 100 MM
REMARK 210 PHOSPHATE BUFFER; REDUCED WITH
REMARK 210 DITHYONITE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_TOCSY; 2D_NOESY; 2D_
REMARK 210 TOCSY; HNHA; HNHB; 15N-HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : SIMULATED ANNEALING IN THE
REMARK 210 DIHEDRAL ANGLE SPACE IN DYANA IN
REMARK 210 15000 STEPS; 30 STRUCTURES WITH
REMARK 210 THE LOWEST TARGET FUNCTION OUT
REMARK 210 OF A TOTAL NUMBER OF 250
REMARK 210 GENERATED STRUCTURES CONSTITUTE
REMARK 210 THE REM FAMILY - SUBJECT TO
REMARK 210 RESTRAINED ENERGY MINIMIZATION
REMARK 210 IN AMBER
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 250
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 2 ASP A 30 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES
REMARK 500 4 ASP A 30 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES
REMARK 500 4 TYR A 67 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 7 ASP A 30 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES
REMARK 500 8 TYR A 67 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 9 TYR A 67 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 11 CYS A 62 CA - CB - SG ANGL. DEV. = 7.3 DEGREES
REMARK 500 12 ASP A 30 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES
REMARK 500 13 CYS A 59 CA - CB - SG ANGL. DEV. = 6.7 DEGREES
REMARK 500 14 CYS A 62 CA - CB - SG ANGL. DEV. = 8.0 DEGREES
REMARK 500 16 ASP A 30 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 29 TYR A 67 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 LEU A -1 58.11 -109.11
REMARK 500 1 ALA A 10 -65.93 -109.48
REMARK 500 1 CYS A 11 40.18 -74.88
REMARK 500 1 CYS A 14 -63.98 -91.01
REMARK 500 1 ALA A 20 18.90 59.07
REMARK 500 1 LEU A 35 8.78 -61.77
REMARK 500 1 VAL A 39 -60.45 -127.04
REMARK 500 1 THR A 60 -67.62 -145.99
REMARK 500 1 SER A 75 -87.41 -163.92
REMARK 500 1 LYS A 76 53.15 172.43
REMARK 500 1 ALA A 77 -85.27 -160.55
REMARK 500 2 ALA A 10 -66.34 -106.62
REMARK 500 2 CYS A 11 41.10 -78.67
REMARK 500 2 ALA A 20 16.89 59.23
REMARK 500 2 LEU A 35 2.18 -66.18
REMARK 500 2 LYS A 37 -61.96 -125.42
REMARK 500 2 VAL A 39 -55.74 -146.81
REMARK 500 2 ASP A 40 26.62 -69.13
REMARK 500 2 LEU A 50 -146.09 -78.49
REMARK 500 2 MET A 58 -37.21 -174.44
REMARK 500 2 THR A 60 -60.67 -128.10
REMARK 500 2 GLU A 65 -64.29 -28.92
REMARK 500 2 SER A 75 -89.91 -152.72
REMARK 500 2 LYS A 76 54.96 169.17
REMARK 500 2 ALA A 77 -87.72 -167.22
REMARK 500 3 ASP A -2 82.68 -164.06
REMARK 500 3 LEU A -1 36.11 -77.18
REMARK 500 3 CYS A 11 40.63 -75.56
REMARK 500 3 CYS A 14 -61.09 -104.06
REMARK 500 3 ALA A 20 35.40 -83.75
REMARK 500 3 VAL A 39 -57.97 -144.09
REMARK 500 3 ASP A 40 6.73 -63.89
REMARK 500 3 MET A 58 44.97 77.58
REMARK 500 3 THR A 60 -88.14 -108.78
REMARK 500 3 ASP A 61 74.93 -106.14
REMARK 500 3 SER A 75 46.67 -167.27
REMARK 500 3 LYS A 76 60.71 37.88
REMARK 500 3 ALA A 77 -82.00 -162.31
REMARK 500 4 ASP A -2 27.71 -160.87
REMARK 500 4 ALA A 10 -67.73 -103.46
REMARK 500 4 CYS A 11 38.73 -76.54
REMARK 500 4 CYS A 14 -61.26 -99.46
REMARK 500 4 VAL A 39 -55.82 -149.02
REMARK 500 4 ASP A 40 28.88 -71.76
REMARK 500 4 LEU A 50 -152.90 -78.02
REMARK 500 4 MET A 58 -0.85 62.83
REMARK 500 4 THR A 60 -71.34 65.54
REMARK 500 4 SER A 75 33.81 -164.07
REMARK 500 4 LYS A 76 61.27 38.23
REMARK 500 4 ALA A 77 -55.57 -149.49
REMARK 500
REMARK 500 THIS ENTRY HAS 362 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ALA A -3 ASP A -2 13 -149.35
REMARK 500 ALA A -3 ASP A -2 25 -144.42
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 TYR A 7 0.10 SIDE CHAIN
REMARK 500 2 TYR A 7 0.09 SIDE CHAIN
REMARK 500 3 TYR A 7 0.10 SIDE CHAIN
REMARK 500 3 ARG A 34 0.14 SIDE CHAIN
REMARK 500 3 TYR A 67 0.10 SIDE CHAIN
REMARK 500 4 TYR A 7 0.12 SIDE CHAIN
REMARK 500 4 TYR A 67 0.10 SIDE CHAIN
REMARK 500 5 TYR A 7 0.08 SIDE CHAIN
REMARK 500 5 TYR A 67 0.16 SIDE CHAIN
REMARK 500 6 TYR A 7 0.07 SIDE CHAIN
REMARK 500 6 TYR A 67 0.07 SIDE CHAIN
REMARK 500 7 TYR A 7 0.10 SIDE CHAIN
REMARK 500 7 TYR A 67 0.08 SIDE CHAIN
REMARK 500 8 TYR A 7 0.07 SIDE CHAIN
REMARK 500 8 TYR A 67 0.12 SIDE CHAIN
REMARK 500 9 TYR A 7 0.09 SIDE CHAIN
REMARK 500 9 TYR A 67 0.15 SIDE CHAIN
REMARK 500 10 TYR A 7 0.09 SIDE CHAIN
REMARK 500 10 TYR A 67 0.06 SIDE CHAIN
REMARK 500 11 TYR A 7 0.12 SIDE CHAIN
REMARK 500 12 TYR A 7 0.10 SIDE CHAIN
REMARK 500 13 TYR A 7 0.09 SIDE CHAIN
REMARK 500 14 TYR A 7 0.09 SIDE CHAIN
REMARK 500 15 TYR A 7 0.08 SIDE CHAIN
REMARK 500 15 TYR A 67 0.14 SIDE CHAIN
REMARK 500 16 TYR A 7 0.12 SIDE CHAIN
REMARK 500 17 TYR A 7 0.08 SIDE CHAIN
REMARK 500 17 TYR A 67 0.08 SIDE CHAIN
REMARK 500 18 TYR A 7 0.10 SIDE CHAIN
REMARK 500 18 ARG A 34 0.09 SIDE CHAIN
REMARK 500 18 TYR A 67 0.08 SIDE CHAIN
REMARK 500 19 TYR A 7 0.09 SIDE CHAIN
REMARK 500 19 ARG A 34 0.15 SIDE CHAIN
REMARK 500 19 TYR A 67 0.10 SIDE CHAIN
REMARK 500 20 TYR A 7 0.10 SIDE CHAIN
REMARK 500 21 TYR A 7 0.08 SIDE CHAIN
REMARK 500 21 ARG A 34 0.10 SIDE CHAIN
REMARK 500 21 TYR A 67 0.18 SIDE CHAIN
REMARK 500 22 ARG A 34 0.16 SIDE CHAIN
REMARK 500 23 TYR A 7 0.11 SIDE CHAIN
REMARK 500 24 TYR A 7 0.11 SIDE CHAIN
REMARK 500 24 ARG A 34 0.13 SIDE CHAIN
REMARK 500 25 TYR A 7 0.10 SIDE CHAIN
REMARK 500 27 TYR A 7 0.12 SIDE CHAIN
REMARK 500 27 TYR A 67 0.07 SIDE CHAIN
REMARK 500 28 TYR A 67 0.09 SIDE CHAIN
REMARK 500 29 TYR A 7 0.10 SIDE CHAIN
REMARK 500 29 TYR A 67 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 HEC A 90 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 15 NE2
REMARK 620 2 HEC A 90 NA 93.4
REMARK 620 3 HEC A 90 NB 87.8 90.2
REMARK 620 4 HEC A 90 NC 88.8 177.2 91.7
REMARK 620 5 HEC A 90 ND 88.6 89.5 176.4 88.8
REMARK 620 6 MET A 53 SD 170.6 83.7 101.1 93.8 82.5
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 90
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1KX2 RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE OF S. PUTREFACIENS MONO-HEME C-TYPE
REMARK 900 CYTOCHROME SCYA
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RECOMBINANT PROTEIN, WITHOUT THE SIGNALING PEPTIDE.
REMARK 999 THE FIRST THREE AMINO-ACIDS (ALA ASP LEU) HAVE
REMARK 999 BEEN ADDED FOR PROTEIN EXPRESSION PURPOSES.
DBREF 1KX7 A 1 78 UNP O52685 O52685_SHEPU 22 99
SEQADV 1KX7 ALA A -3 UNP O52685 CLONING ARTIFACT
SEQADV 1KX7 ASP A -2 UNP O52685 CLONING ARTIFACT
SEQADV 1KX7 LEU A -1 UNP O52685 CLONING ARTIFACT
SEQRES 1 A 81 ALA ASP LEU GLN ASP ALA GLU ALA ILE TYR ASN LYS ALA
SEQRES 2 A 81 CYS THR VAL CYS HIS SER MET GLY VAL ALA GLY ALA PRO
SEQRES 3 A 81 LYS SER HIS ASN THR ALA ASP TRP GLU PRO ARG LEU ALA
SEQRES 4 A 81 LYS GLY VAL ASP ASN LEU VAL LYS SER VAL LYS THR GLY
SEQRES 5 A 81 LEU ASN ALA MET PRO PRO GLY GLY MET CYS THR ASP CYS
SEQRES 6 A 81 THR ASP GLU ASP TYR LYS ALA ALA ILE GLU PHE MET SER
SEQRES 7 A 81 LYS ALA LYS
HET HEC A 90 75
HETNAM HEC HEME C
FORMUL 2 HEC C34 H34 FE N4 O4
HELIX 1 1 ASP A 2 ALA A 10 1 9
HELIX 2 2 VAL A 39 GLY A 49 1 11
HELIX 3 3 THR A 63 SER A 75 1 13
SSBOND 1 CYS A 59 CYS A 62 1555 1555 2.10
LINK SG CYS A 11 CAB HEC A 90 1555 1555 1.81
LINK SG CYS A 14 CAC HEC A 90 1555 1555 1.83
LINK NE2 HIS A 15 FE HEC A 90 1555 1555 1.97
LINK SD MET A 53 FE HEC A 90 1555 1555 2.36
SITE 1 AC1 16 ALA A 10 CYS A 11 CYS A 14 HIS A 15
SITE 2 AC1 16 ALA A 20 ALA A 22 PRO A 23 ARG A 34
SITE 3 AC1 16 LEU A 42 VAL A 46 LEU A 50 ALA A 52
SITE 4 AC1 16 MET A 53 GLY A 57 ILE A 71 LYS A 78
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - b 23 2 Bytes