Header list of 1rjv.pdb file
Complete list - r 2 2 Bytes
HEADER METAL BINDING PROTEIN 20-NOV-03 1RJV
TITLE SOLUTION STRUCTURE OF HUMAN ALPHA-PARVALBUMIN REFINED WITH A
TITLE 2 PARAMAGNETISM-BASED STRATEGY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PARVALBUMIN ALPHA;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PVALB;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE-30 XA
KEYWDS CALCIUM, PARVALBUMIN, EF-HAND, LANTHANIDE, STRUCTURAL PROTEOMICS IN
KEYWDS 2 EUROPE, SPINE, STRUCTURAL GENOMICS, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 19
AUTHOR I.BAIG,I.BERTINI,C.DEL BIANCO,Y.K.GUPTA,Y.M.LEE,C.LUCHINAT,
AUTHOR 2 A.QUATTRONE,STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
REVDAT 3 02-MAR-22 1RJV 1 REMARK LINK
REVDAT 2 24-FEB-09 1RJV 1 VERSN
REVDAT 1 25-MAY-04 1RJV 0
JRNL AUTH I.BAIG,I.BERTINI,C.DEL BIANCO,Y.K.GUPTA,Y.M.LEE,C.LUCHINAT,
JRNL AUTH 2 A.QUATTRONE
JRNL TITL PARAMAGNETISM-BASED REFINEMENT STRATEGY FOR THE SOLUTION
JRNL TITL 2 STRUCTURE OF HUMAN ALPHA-PARVALBUMIN.
JRNL REF BIOCHEMISTRY V. 43 5562 2004
JRNL REFN ISSN 0006-2960
JRNL PMID 15122922
JRNL DOI 10.1021/BI035879K
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.1, AMBER 5.0
REMARK 3 AUTHORS : BRUNGER (XWINNMR), PEARLMAN (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1RJV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-03.
REMARK 100 THE DEPOSITION ID IS D_1000020817.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298
REMARK 210 PH : 7; 7; 7; 7
REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL; 100 MM
REMARK 210 NACL; 100 MM NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT;
REMARK 210 AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.5MM PARVALBUMIN U-15N,13C;
REMARK 210 100MM NACL; 90% H2O, 10% D2O; PH
REMARK 210 7; FOR CACAPV; 0.6MM PARVALBUMIN
REMARK 210 U-15N; 100MM NACL; 90% H2O, 10%
REMARK 210 D2O; PH 7; FOR CACAPV; 1.5MM
REMARK 210 PARVALBUMIN U-15N,13C; 100MM
REMARK 210 NACL; 90% H2O, 10% D2O; PH 7;
REMARK 210 FOR CADYPV; 0.6MM PARVALBUMIN U-
REMARK 210 15N; 100MM NACL; 90% H2O, 10%
REMARK 210 D2O; PH 7; FOR CADYPV
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; 2D NOESY; 2D
REMARK 210 TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 3.1, XEASY 1.3, DYANA
REMARK 210 1.5
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING, TORSION ANGLE
REMARK 210 DYNAMICS, PSEUDOCONTACT SHIFTS,
REMARK 210 RESIDUAL DIPOLAR COUPLING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING DIAMAGNETIC,
REMARK 210 PSEUDOCONTACT SHIFT AND RESIDUAL DIPOLAR COUPLING CONSTRAINTS
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OD2 ASP A 23 HG SER A 79 1.33
REMARK 500 OE1 GLU A 61 HG1 THR A 83 1.38
REMARK 500 HG1 THR A 22 OD1 ASP A 23 1.38
REMARK 500 O PHE A 71 HG SER A 72 1.58
REMARK 500
REMARK 500 REMARK: NULL
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 1 ASP A 95 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 18 ASP A 54 CB - CG - OD2 ANGL. DEV. = 5.4 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 SER A 2 81.95 118.80
REMARK 500 1 THR A 4 -50.53 -174.71
REMARK 500 1 LEU A 7 -106.31 -90.86
REMARK 500 1 ASN A 8 117.37 -176.57
REMARK 500 1 SER A 24 48.47 -86.07
REMARK 500 1 VAL A 47 -72.84 -59.15
REMARK 500 1 PHE A 66 25.76 -148.74
REMARK 500 1 SER A 72 173.95 177.12
REMARK 500 1 ARG A 76 170.50 73.36
REMARK 500 2 SER A 2 71.62 -174.93
REMARK 500 2 THR A 4 -52.64 176.70
REMARK 500 2 LEU A 7 -84.64 -114.01
REMARK 500 2 ASN A 8 111.07 170.66
REMARK 500 2 SER A 20 59.52 -67.59
REMARK 500 2 ASP A 23 -4.04 73.95
REMARK 500 2 SER A 24 41.44 -86.23
REMARK 500 2 ASP A 52 48.82 -65.08
REMARK 500 2 LYS A 55 78.56 54.14
REMARK 500 2 PHE A 66 40.98 -147.09
REMARK 500 2 SER A 72 173.08 178.08
REMARK 500 2 ASP A 74 7.57 56.82
REMARK 500 2 ALA A 75 -70.87 -13.94
REMARK 500 2 ARG A 76 -177.95 63.90
REMARK 500 3 SER A 2 99.66 64.94
REMARK 500 3 THR A 4 -49.83 -172.86
REMARK 500 3 LEU A 7 -117.76 -69.11
REMARK 500 3 ASP A 23 18.98 57.36
REMARK 500 3 PHE A 25 85.54 -41.84
REMARK 500 3 ASP A 26 44.97 -78.16
REMARK 500 3 ASP A 52 88.19 -69.24
REMARK 500 3 LYS A 53 35.23 -80.83
REMARK 500 3 ASP A 54 -39.00 -161.24
REMARK 500 3 LYS A 55 -3.14 103.74
REMARK 500 3 PHE A 66 43.99 -153.95
REMARK 500 3 ARG A 76 171.65 63.58
REMARK 500 4 SER A 2 -149.80 82.66
REMARK 500 4 MET A 3 96.99 -48.25
REMARK 500 4 THR A 4 -60.17 159.40
REMARK 500 4 LEU A 7 -83.96 -86.69
REMARK 500 4 ASN A 8 115.10 161.97
REMARK 500 4 SER A 20 66.65 -64.18
REMARK 500 4 THR A 22 -72.68 -76.99
REMARK 500 4 LYS A 53 23.24 -70.35
REMARK 500 4 PHE A 66 39.84 -144.49
REMARK 500 4 SER A 72 173.60 178.33
REMARK 500 4 ALA A 75 81.70 -59.30
REMARK 500 4 ASP A 91 71.71 -69.21
REMARK 500 5 SER A 2 61.56 137.36
REMARK 500 5 THR A 4 -51.13 178.58
REMARK 500 5 LEU A 7 -78.21 -95.33
REMARK 500
REMARK 500 THIS ENTRY HAS 211 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 ASP A 74 ALA A 75 2 139.42
REMARK 500 ALA A 108 GLU A 109 18 146.26
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 ARG A 76 0.08 SIDE CHAIN
REMARK 500 2 ARG A 76 0.10 SIDE CHAIN
REMARK 500 6 ARG A 76 0.09 SIDE CHAIN
REMARK 500 8 ARG A 76 0.09 SIDE CHAIN
REMARK 500 16 PHE A 48 0.09 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 CA A 112 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 52 OD1
REMARK 620 2 ASP A 54 OD2 108.2
REMARK 620 3 SER A 56 OG 68.5 78.0
REMARK 620 4 PHE A 58 O 68.6 152.5 75.5
REMARK 620 5 GLU A 60 OE1 146.7 104.0 127.6 86.5
REMARK 620 6 GLU A 60 OE2 133.4 100.6 83.1 68.9 44.6
REMARK 620 7 GLU A 63 OE1 80.2 104.8 147.5 101.5 83.8 126.7
REMARK 620 8 GLU A 63 OE2 73.9 68.3 117.2 131.8 111.5 152.3 41.8
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 111 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 91 OD1
REMARK 620 2 ASP A 93 OD2 105.6
REMARK 620 3 ASP A 95 OD1 69.5 137.1
REMARK 620 4 ASP A 95 OD2 95.2 82.1 57.0
REMARK 620 5 LYS A 97 O 75.0 148.4 73.6 129.5
REMARK 620 6 GLU A 102 OE1 72.2 63.1 140.5 136.7 88.1
REMARK 620 7 GLU A 102 OE2 109.2 71.7 151.1 147.9 78.3 42.5
REMARK 620 N 1 2 3 4 5 6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 111
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 112
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: CIRMMP07 RELATED DB: TARGETDB
DBREF 1RJV A 1 110 UNP P20472 PRVA_HUMAN 0 109
SEQRES 1 A 110 MET SER MET THR ASP LEU LEU ASN ALA GLU ASP ILE LYS
SEQRES 2 A 110 LYS ALA VAL GLY ALA PHE SER ALA THR ASP SER PHE ASP
SEQRES 3 A 110 HIS LYS LYS PHE PHE GLN MET VAL GLY LEU LYS LYS LYS
SEQRES 4 A 110 SER ALA ASP ASP VAL LYS LYS VAL PHE HIS MET LEU ASP
SEQRES 5 A 110 LYS ASP LYS SER GLY PHE ILE GLU GLU ASP GLU LEU GLY
SEQRES 6 A 110 PHE ILE LEU LYS GLY PHE SER PRO ASP ALA ARG ASP LEU
SEQRES 7 A 110 SER ALA LYS GLU THR LYS MET LEU MET ALA ALA GLY ASP
SEQRES 8 A 110 LYS ASP GLY ASP GLY LYS ILE GLY VAL ASP GLU PHE SER
SEQRES 9 A 110 THR LEU VAL ALA GLU SER
HET CA A 111 1
HET CA A 112 1
HETNAM CA CALCIUM ION
FORMUL 2 CA 2(CA 2+)
HELIX 1 1 ASN A 8 PHE A 19 1 12
HELIX 2 2 ASP A 26 VAL A 34 1 9
HELIX 3 3 GLY A 35 LYS A 39 5 5
HELIX 4 4 SER A 40 ASP A 52 1 13
HELIX 5 5 GLU A 60 GLY A 65 1 6
HELIX 6 6 ILE A 67 SER A 72 1 6
HELIX 7 7 SER A 79 ASP A 91 1 13
HELIX 8 8 GLY A 99 VAL A 107 1 9
LINK OD1 ASP A 52 CA CA A 112 1555 1555 3.00
LINK OD2 ASP A 54 CA CA A 112 1555 1555 2.33
LINK OG SER A 56 CA CA A 112 1555 1555 3.18
LINK O PHE A 58 CA CA A 112 1555 1555 2.51
LINK OE1 GLU A 60 CA CA A 112 1555 1555 2.15
LINK OE2 GLU A 60 CA CA A 112 1555 1555 3.09
LINK OE1 GLU A 63 CA CA A 112 1555 1555 2.43
LINK OE2 GLU A 63 CA CA A 112 1555 1555 3.27
LINK OD1 ASP A 91 CA CA A 111 1555 1555 3.06
LINK OD2 ASP A 93 CA CA A 111 1555 1555 3.02
LINK OD1 ASP A 95 CA CA A 111 1555 1555 2.23
LINK OD2 ASP A 95 CA CA A 111 1555 1555 2.18
LINK O LYS A 97 CA CA A 111 1555 1555 3.04
LINK OE1 GLU A 102 CA CA A 111 1555 1555 3.22
LINK OE2 GLU A 102 CA CA A 111 1555 1555 2.15
SITE 1 AC1 5 ASP A 91 ASP A 93 ASP A 95 LYS A 97
SITE 2 AC1 5 GLU A 102
SITE 1 AC2 6 ASP A 52 ASP A 54 SER A 56 PHE A 58
SITE 2 AC2 6 GLU A 60 GLU A 63
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 - r 2 2 Bytes