PDB Short entry for 1EYF 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