Header list of 1eyf.pdb file
Complete list - b 16 2 Bytes
HEADER DNA BINDING PROTEIN 06-MAY-00 1EYF
TITLE REFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN OF
TITLE 2 E. COLI ADA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ADA REGULATORY PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: N-TERMINAL 10 KDA DOMAIN;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PADA39
KEYWDS ONE CENTRAL BETA-SHEET SANDWICHED BETWEEN TWO ALPHA-HELICES, DNA
KEYWDS 2 BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 25
AUTHOR Y.LIN,V.DOTSCH,T.WINTNER,K.PEARISO,L.C.MYERS,J.E.PENNER-HAHN,
AUTHOR 2 G.L.VERDINE,G.WAGNER
REVDAT 3 16-FEB-22 1EYF 1 REMARK LINK
REVDAT 2 24-FEB-09 1EYF 1 VERSN
REVDAT 1 09-SEP-03 1EYF 0
JRNL AUTH Y.LIN,V.DOTSCH,T.WINTNER,K.PEARISO,L.C.MYERS,
JRNL AUTH 2 J.E.PENNER-HAHN,G.L.VERDINE,G.WAGNER
JRNL TITL STRUCTURAL BASIS FOR THE FUNCTIONAL SWITCH OF THE E. COLI
JRNL TITL 2 ADA PROTEIN
JRNL REF BIOCHEMISTRY V. 40 4261 2001
JRNL REFN ISSN 0006-2960
JRNL PMID 11284682
JRNL DOI 10.1021/BI002109P
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : UXNMR, DGII
REMARK 3 AUTHORS : HAVEL ET AL (DGII)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1014 RESTRAINTS, 872 ARE
REMARK 3 NOE-DERIVED
REMARK 3 DISTANCE CONSTRAINTS, 82 DIHEDRAL ANGLE RESTRAINTS,46 DISTANCE
REMARK 3 RESTRAINTS
REMARK 3 FROM HYDROGEN BONDS, AND 14 ZINC CLUSTER DISTANCE RESTRAINTS
REMARK 4
REMARK 4 1EYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-00.
REMARK 100 THE DEPOSITION ID IS D_1000011024.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298
REMARK 210 PH : 6.4; 6.4; 6.4; 6.4
REMARK 210 IONIC STRENGTH : NULL; NULL; NULL; NULL
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT;
REMARK 210 AMBIENT
REMARK 210 SAMPLE CONTENTS : 2 MM N-ADA10; 25 MM SODIUM
REMARK 210 PHOSPHATE BUFFER PH 6.4, 50 MM
REMARK 210 NACL, AND 10 MM 2-
REMARK 210 MERCAPTOETHANOL; 90% H2O, 10%
REMARK 210 D2O; 2 MM N-ADA10; 25 MM SODIUM
REMARK 210 PHOSPHATE BUFFER PH 6.4, 50 MM
REMARK 210 NACL, AND 10 MM 2-
REMARK 210 MERCAPTOETHANOL; 100% D2O; 2 MM
REMARK 210 N-ADA10 U-15N; 25 MM SODIUM
REMARK 210 PHOSPHATE BUFFER PH 6.4, 50 MM
REMARK 210 NACL, AND 10 MM 2-
REMARK 210 MERCAPTOETHANOL; 90% H2O, 10%
REMARK 210 D2O; 2 MM N-ADA10 U-15N, 13C; 25
REMARK 210 MM SODIUM PHOSPHATE BUFFER PH
REMARK 210 6.4, 50 MM NACL, AND 10 MM 2-
REMARK 210 MERCAPTOETHANOL; 90% H2O, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; HNHA
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 400 MHZ; 750
REMARK 210 MHZ
REMARK 210 SPECTROMETER MODEL : AMX; VXRS; UNITY; UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR, FELIX 95, XEASY, DGII
REMARK 210 METHOD USED : DISTANCE GEOMETRY
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 13
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR AND 3D HETERONUCLEAR TECHINQUES
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 HG21 VAL A 31 HG22 VAL A 52 1.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 1 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 2 ARG A 92 C ARG A 92 OXT 0.200
REMARK 500 3 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 4 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 5 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 6 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 7 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 8 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 9 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 10 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 11 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 12 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 13 ARG A 92 C ARG A 92 OXT 0.200
REMARK 500 14 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 15 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 16 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 17 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 18 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 19 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 20 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 21 ARG A 92 C ARG A 92 OXT 0.200
REMARK 500 22 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 23 ARG A 92 C ARG A 92 OXT 0.201
REMARK 500 24 ARG A 92 C ARG A 92 OXT 0.200
REMARK 500 25 ARG A 92 C ARG A 92 OXT 0.201
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 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 3 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 4 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 5 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 6 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 7 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 8 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 9 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 10 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 11 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 12 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 13 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 14 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 15 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 16 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 17 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 18 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 19 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 20 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 21 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 22 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 23 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 24 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 25 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 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 LYS A 3 151.74 168.24
REMARK 500 1 ALA A 4 47.65 172.87
REMARK 500 1 THR A 5 -96.13 47.17
REMARK 500 1 ASP A 10 -75.93 -41.67
REMARK 500 1 ARG A 19 30.23 76.55
REMARK 500 1 ASP A 20 89.17 -51.21
REMARK 500 1 PHE A 27 -174.95 -177.98
REMARK 500 1 CYS A 42 94.72 -60.64
REMARK 500 1 ARG A 45 106.78 -45.48
REMARK 500 1 ASP A 75 62.30 75.87
REMARK 500 1 LYS A 76 45.97 -103.17
REMARK 500 1 PRO A 79 -88.54 -73.57
REMARK 500 1 ARG A 80 -70.77 -23.19
REMARK 500 1 GLN A 81 123.28 -15.97
REMARK 500 1 HIS A 82 134.47 -28.52
REMARK 500 1 ARG A 83 56.01 -97.35
REMARK 500 1 LEU A 84 154.29 -42.43
REMARK 500 1 ASP A 85 -81.76 -39.86
REMARK 500 1 LYS A 86 -48.52 167.04
REMARK 500 1 HIS A 89 93.15 59.44
REMARK 500 2 ALA A 4 -56.19 170.94
REMARK 500 2 THR A 5 -84.45 89.54
REMARK 500 2 CYS A 6 48.19 -102.29
REMARK 500 2 ASP A 20 98.38 -66.18
REMARK 500 2 ASP A 24 -98.47 -40.93
REMARK 500 2 PHE A 27 -178.06 -175.85
REMARK 500 2 PRO A 40 -18.10 -49.32
REMARK 500 2 ARG A 45 105.79 -43.16
REMARK 500 2 ARG A 71 -42.97 -135.19
REMARK 500 2 CYS A 72 -72.92 -102.32
REMARK 500 2 PRO A 74 -98.97 -92.40
REMARK 500 2 ASP A 75 49.58 177.30
REMARK 500 2 LYS A 76 37.65 -90.78
REMARK 500 2 ASN A 78 56.31 -145.20
REMARK 500 2 ARG A 80 -71.21 -20.93
REMARK 500 2 GLN A 81 -177.07 59.21
REMARK 500 2 ARG A 83 91.73 48.39
REMARK 500 2 LEU A 84 108.30 179.50
REMARK 500 2 ASP A 85 -145.30 -148.44
REMARK 500 2 LYS A 86 -172.67 64.48
REMARK 500 2 ALA A 90 -174.21 62.63
REMARK 500 3 ALA A 4 -156.19 177.65
REMARK 500 3 CYS A 6 62.79 -100.51
REMARK 500 3 ASP A 10 -72.95 -42.38
REMARK 500 3 ASP A 20 99.32 -55.46
REMARK 500 3 PHE A 27 -178.70 -172.68
REMARK 500 3 CYS A 42 90.98 -63.45
REMARK 500 3 PRO A 79 104.96 -46.72
REMARK 500 3 ARG A 80 -162.24 -38.40
REMARK 500 3 GLN A 81 84.50 5.15
REMARK 500
REMARK 500 THIS ENTRY HAS 476 RAMACHANDRAN OUTLIERS.
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 ZN A 93 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 38 SG
REMARK 620 2 CYS A 42 SG 114.4
REMARK 620 3 CYS A 69 SG 94.0 128.5
REMARK 620 4 CYS A 72 SG 103.5 96.6 118.3
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 93
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1ADN RELATED DB: PDB
REMARK 900 1ADN CONTAINS THE PRELIMINARY STRUCTURES OF THE SAME PROTEIN ON
REMARK 900 WHICH THE REFINED STRUCTURES ARE BASED
DBREF 1EYF A 1 92 UNP P06134 ADA_ECOLI 1 92
SEQRES 1 A 92 MET LYS LYS ALA THR CYS LEU THR ASP ASP GLN ARG TRP
SEQRES 2 A 92 GLN SER VAL LEU ALA ARG ASP PRO ASN ALA ASP GLY GLU
SEQRES 3 A 92 PHE VAL PHE ALA VAL ARG THR THR GLY ILE PHE CYS ARG
SEQRES 4 A 92 PRO SER CYS ARG ALA ARG HIS ALA LEU ARG GLU ASN VAL
SEQRES 5 A 92 SER PHE TYR ALA ASN ALA SER GLU ALA LEU ALA ALA GLY
SEQRES 6 A 92 PHE ARG PRO CYS LYS ARG CYS GLN PRO ASP LYS ALA ASN
SEQRES 7 A 92 PRO ARG GLN HIS ARG LEU ASP LYS ILE THR HIS ALA CYS
SEQRES 8 A 92 ARG
HET ZN A 93 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 THR A 8 ALA A 18 1 11
HELIX 2 2 LEU A 48 GLU A 50 5 3
HELIX 3 3 ASN A 57 ALA A 64 1 8
SHEET 1 A 4 VAL A 52 TYR A 55 0
SHEET 2 A 4 VAL A 28 VAL A 31 -1 O VAL A 28 N TYR A 55
SHEET 3 A 4 ILE A 36 CYS A 38 -1 O ILE A 36 N VAL A 31
SHEET 4 A 4 ARG A 67 PRO A 68 1 O ARG A 67 N PHE A 37
LINK SG CYS A 38 ZN ZN A 93 1555 1555 2.35
LINK SG CYS A 42 ZN ZN A 93 1555 1555 2.24
LINK SG CYS A 69 ZN ZN A 93 1555 1555 2.36
LINK SG CYS A 72 ZN ZN A 93 1555 1555 2.37
SITE 1 AC1 4 CYS A 38 CYS A 42 CYS A 69 CYS A 72
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 16 2 Bytes