Header list of 2avx.pdb file
Complete list - t 20 2 Bytes
HEADER TRANSCRIPTION 30-AUG-05 2AVX
TITLE SOLUTION STRUCTURE OF E COLI SDIA1-171
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: REGULATORY PROTEIN SDIA;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: SDIA;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: EL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A
KEYWDS HOMOSERINE LACTONE, QUORUM SENSING, TRANSCRIPTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR Y.YAO,M.A.MARTINEZ-YAMOUT,T.J.DICKERSON,A.P.BROGAN,P.E.WRIGHT,
AUTHOR 2 H.J.DYSON
REVDAT 3 20-OCT-21 2AVX 1 REMARK SEQADV
REVDAT 2 24-FEB-09 2AVX 1 VERSN
REVDAT 1 20-JUN-06 2AVX 0
JRNL AUTH Y.YAO,M.A.MARTINEZ-YAMOUT,T.J.DICKERSON,A.P.BROGAN,
JRNL AUTH 2 P.E.WRIGHT,H.J.DYSON
JRNL TITL STRUCTURE OF THE ESCHERICHIA COLI QUORUM SENSING PROTEIN
JRNL TITL 2 SDIA: ACTIVATION OF THE FOLDING SWITCH BY ACYL HOMOSERINE
JRNL TITL 3 LACTONES.
JRNL REF J.MOL.BIOL. V. 355 262 2006
JRNL REFN ISSN 0022-2836
JRNL PMID 16307757
JRNL DOI 10.1016/J.JMB.2005.10.041
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 1.5, AMBER 8.0
REMARK 3 AUTHORS :
REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH,
REMARK 3 WEINER,KOLLMAN (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2AVX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-05.
REMARK 100 THE DEPOSITION ID IS D_1000034376.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 4.2
REMARK 210 IONIC STRENGTH : 50MM
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : 0.2 MM 13C, 15N LABELED
REMARK 210 PROTEIN,50MM SODIUM ACETIC, 2MM
REMARK 210 DTT, 1MM EDTA, 0.2M UREA,PH 4.2,
REMARK 210 H2O; 0.2 MM 13C, 15N LABELED
REMARK 210 PROTEIN,50MM SODIUM ACETIC, 2MM
REMARK 210 DTT, 1MM EDTA, 0.2M UREA,PH 4.2,
REMARK 210 D2O; 0.3 MM 13C, 15N, 2H LABELED
REMARK 210 PROTEIN,50MM SODIUM ACETIC, 2MM
REMARK 210 DTT, 1MM EDTA, 0.2M UREA,PH 4.2,
REMARK 210 H2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; HNCA; HNCO;
REMARK 210 HN(CO)CA; HNCB
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ; 900
REMARK 210 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
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: 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 5 ARG A 137 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 5 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 8 ARG A 116 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 11 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 14 ARG A 116 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 15 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 15 ARG A 10 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 15 TYR A 63 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 16 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 16 ARG A 159 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES
REMARK 500 16 ARG A 159 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 20 ARG A 159 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 20 ARG A 167 NE - CZ - NH1 ANGL. DEV. = 3.2 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 30.49 -161.07
REMARK 500 1 LYS A 4 12.12 -142.34
REMARK 500 1 GLU A 21 -9.60 67.29
REMARK 500 1 ASP A 40 -93.63 163.76
REMARK 500 1 ALA A 103 42.71 -74.88
REMARK 500 1 ARG A 128 -136.88 115.72
REMARK 500 1 ALA A 129 -173.31 52.11
REMARK 500 1 SER A 139 99.51 -67.44
REMARK 500 1 ALA A 140 6.90 -69.03
REMARK 500 1 PRO A 144 -125.71 -84.41
REMARK 500 1 ILE A 145 26.86 -76.09
REMARK 500 1 LEU A 146 -42.75 75.57
REMARK 500 1 SER A 147 122.03 120.32
REMARK 500 1 ASP A 170 -15.71 67.19
REMARK 500 2 SER A 2 84.90 129.19
REMARK 500 2 LYS A 4 -3.66 70.68
REMARK 500 2 ASP A 40 -82.87 155.47
REMARK 500 2 ALA A 103 45.88 -79.08
REMARK 500 2 ARG A 117 138.90 -174.76
REMARK 500 2 GLU A 127 76.73 -159.37
REMARK 500 2 ARG A 128 -178.25 165.67
REMARK 500 2 PRO A 144 -84.37 -80.93
REMARK 500 2 LEU A 146 -25.08 104.21
REMARK 500 2 SER A 147 120.69 95.33
REMARK 500 2 ASP A 170 -12.52 54.22
REMARK 500 3 SER A 2 36.07 157.01
REMARK 500 3 LYS A 4 -1.59 83.31
REMARK 500 3 ASP A 40 -85.81 161.58
REMARK 500 3 ALA A 103 41.76 -78.60
REMARK 500 3 GLU A 127 48.81 -81.03
REMARK 500 3 ILE A 145 34.52 -153.76
REMARK 500 3 LEU A 146 -37.30 70.43
REMARK 500 3 SER A 147 132.16 114.33
REMARK 500 3 ASP A 170 10.38 51.52
REMARK 500 4 LYS A 4 -10.77 68.47
REMARK 500 4 GLU A 21 -16.21 69.68
REMARK 500 4 ASP A 40 -94.35 167.54
REMARK 500 4 ALA A 103 36.93 -89.26
REMARK 500 4 ARG A 128 94.03 128.87
REMARK 500 4 PRO A 144 -109.65 -86.26
REMARK 500 4 LEU A 146 -49.22 79.35
REMARK 500 4 SER A 147 123.48 134.24
REMARK 500 4 ASP A 170 -19.66 62.65
REMARK 500 5 LYS A 4 -3.15 -158.39
REMARK 500 5 ASP A 40 -84.96 137.92
REMARK 500 5 ALA A 103 38.58 -73.65
REMARK 500 5 ARG A 128 163.11 94.32
REMARK 500 5 ALA A 129 154.48 85.09
REMARK 500 5 CYS A 138 -6.59 -59.32
REMARK 500 5 PRO A 144 -125.28 -86.14
REMARK 500
REMARK 500 THIS ENTRY HAS 195 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 129 LEU A 130 1 146.27
REMARK 500 MET A 1 SER A 2 3 -140.38
REMARK 500 SER A 2 ASP A 3 6 147.75
REMARK 500 SER A 2 ASP A 3 10 -148.17
REMARK 500 LEU A 146 SER A 147 11 -148.59
REMARK 500 SER A 2 ASP A 3 12 -139.71
REMARK 500 ASP A 3 LYS A 4 12 149.82
REMARK 500 SER A 2 ASP A 3 15 -140.21
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 42 0.07 SIDE CHAIN
REMARK 500 1 ARG A 128 0.08 SIDE CHAIN
REMARK 500 3 TYR A 42 0.09 SIDE CHAIN
REMARK 500 5 TYR A 63 0.08 SIDE CHAIN
REMARK 500 9 TYR A 39 0.08 SIDE CHAIN
REMARK 500 10 TYR A 71 0.09 SIDE CHAIN
REMARK 500 11 TYR A 71 0.07 SIDE CHAIN
REMARK 500 14 ARG A 128 0.08 SIDE CHAIN
REMARK 500 18 TYR A 42 0.09 SIDE CHAIN
REMARK 500 18 TYR A 71 0.12 SIDE CHAIN
REMARK 500 19 TYR A 42 0.07 SIDE CHAIN
REMARK 500 19 TYR A 71 0.08 SIDE CHAIN
REMARK 500 19 ARG A 111 0.09 SIDE CHAIN
REMARK 500 19 ARG A 167 0.18 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HTF A 172
DBREF 2AVX A 1 171 UNP P07026 SDIA_ECOLI 1 171
SEQADV 2AVX SER A 2 UNP P07026 GLN 2 ENGINEERED MUTATION
SEQADV 2AVX GLU A 127 UNP P07026 ASN 127 ENGINEERED MUTATION
SEQRES 1 A 171 MET SER ASP LYS ASP PHE PHE SER TRP ARG ARG THR MET
SEQRES 2 A 171 LEU LEU ARG PHE GLN ARG MET GLU THR ALA GLU GLU VAL
SEQRES 3 A 171 TYR HIS GLU ILE GLU LEU GLN ALA GLN GLN LEU GLU TYR
SEQRES 4 A 171 ASP TYR TYR SER LEU CYS VAL ARG HIS PRO VAL PRO PHE
SEQRES 5 A 171 THR ARG PRO LYS VAL ALA PHE TYR THR ASN TYR PRO GLU
SEQRES 6 A 171 ALA TRP VAL SER TYR TYR GLN ALA LYS ASN PHE LEU ALA
SEQRES 7 A 171 ILE ASP PRO VAL LEU ASN PRO GLU ASN PHE SER GLN GLY
SEQRES 8 A 171 HIS LEU MET TRP ASN ASP ASP LEU PHE SER GLU ALA GLN
SEQRES 9 A 171 PRO LEU TRP GLU ALA ALA ARG ALA HIS GLY LEU ARG ARG
SEQRES 10 A 171 GLY VAL THR GLN TYR LEU MET LEU PRO GLU ARG ALA LEU
SEQRES 11 A 171 GLY PHE LEU SER PHE SER ARG CYS SER ALA ARG GLU ILE
SEQRES 12 A 171 PRO ILE LEU SER ASP GLU LEU GLN LEU LYS MET GLN LEU
SEQRES 13 A 171 LEU VAL ARG GLU SER LEU MET ALA LEU MET ARG LEU ASN
SEQRES 14 A 171 ASP GLU
HET HTF A 172 37
HETNAM HTF N-(2-OXOTETRAHYDROFURAN-3-YL)OCTANAMIDE
HETSYN HTF N-OCTANOYL-L-HOMOSERINE LACTONE
FORMUL 2 HTF C12 H21 N O3
HELIX 1 1 LYS A 4 MET A 20 1 17
HELIX 2 2 THR A 22 GLN A 36 1 15
HELIX 3 3 PRO A 64 LYS A 74 1 11
HELIX 4 4 ASN A 75 ILE A 79 5 5
HELIX 5 5 ASP A 80 ASN A 84 5 5
HELIX 6 6 ALA A 103 GLY A 114 1 12
HELIX 7 7 SER A 147 ASP A 170 1 24
SHEET 1 A 5 LYS A 56 THR A 61 0
SHEET 2 A 5 TYR A 42 HIS A 48 -1 N VAL A 46 O ALA A 58
SHEET 3 A 5 LEU A 130 ARG A 137 -1 O SER A 134 N SER A 43
SHEET 4 A 5 ARG A 117 LEU A 123 -1 N ARG A 117 O ARG A 137
SHEET 5 A 5 HIS A 92 MET A 94 -1 N LEU A 93 O THR A 120
SITE 1 AC1 10 TYR A 63 TRP A 67 TYR A 71 ASP A 80
SITE 2 AC1 10 VAL A 82 TRP A 95 PHE A 100 LEU A 106
SITE 3 AC1 10 ALA A 110 LEU A 115
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 - t 20 2 Bytes