HEADER DNA BINDING PROTEIN 07-SEP-04 1WPK TITLE METHYLATED FORM OF N-TERMINAL TRANSCRIPTIONAL REGULATOR DOMAIN OF TITLE 2 ESCHERICHIA COLI ADA PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADA REGULATORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: METHYLATED N-TERMINAL 16 KDA DOMAIN; COMPND 5 SYNONYM: REGULATORY PROTEIN OF ADAPTATIVE RESPONSE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ADA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS ZINC COORDINATION, HELIX-TURN-HELIX, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR H.TAKINOWAKI,Y.MATSUDA,T.YOSHIDA,Y.KOBAYASHI,T.OHKUBO REVDAT 5 02-MAR-22 1WPK 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 1WPK 1 VERSN REVDAT 3 14-MAR-06 1WPK 1 JRNL REVDAT 2 07-MAR-06 1WPK 1 JRNL REVDAT 1 13-SEP-05 1WPK 0 JRNL AUTH H.TAKINOWAKI,Y.MATSUDA,T.YOSHIDA,Y.KOBAYASHI,T.OHKUBO JRNL TITL THE SOLUTION STRUCTURE OF THE METHYLATED FORM OF THE JRNL TITL 2 N-TERMINAL 16-KDA DOMAIN OF ESCHERICHIA COLI ADA PROTEIN JRNL REF PROTEIN SCI. V. 15 487 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16452614 JRNL DOI 10.1110/PS.051786306 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON, REMARK 3 WARREN (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1991 RESTRAINTS; 1735 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 148 DIHEDRAL ANGLE RESTRAINTS, 94 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS AND 14 ZINC-THIOLATE CENTER DISTANCE REMARK 3 RESTRAINTS. REMARK 4 REMARK 4 1WPK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000023853. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 300MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM PROTEIN U-15N,13C; 50MM REMARK 210 PHOSPHATE BUFFER WITH 5MM 2- REMARK 210 MERCAPTOETHANOL NA; 85% H2O, 15% REMARK 210 D2O; 1MM PROTEIN U-15N,13C; 50MM REMARK 210 PHOSPHATE BUFFER WITH 5MM 2- REMARK 210 MERCAPTOETHANOL ; 99.9% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER MODELS REMARK 210 ARE THE 17 STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 H VAL A 31 O ILE A 36 1.56 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 2 99.37 60.04 REMARK 500 1 LYS A 3 99.62 -66.48 REMARK 500 1 THR A 5 -179.40 -69.93 REMARK 500 1 ASP A 24 91.76 -55.47 REMARK 500 1 GLU A 26 -83.21 -64.96 REMARK 500 1 PHE A 27 139.85 -174.31 REMARK 500 1 ARG A 39 172.39 -48.28 REMARK 500 1 SER A 41 -112.59 -79.26 REMARK 500 1 CYS A 42 151.01 73.08 REMARK 500 1 ARG A 43 24.81 -146.23 REMARK 500 1 ARG A 45 99.09 -58.20 REMARK 500 1 ALA A 47 120.40 62.75 REMARK 500 1 GLU A 50 -38.30 -177.80 REMARK 500 1 GLN A 73 84.40 55.34 REMARK 500 1 GLU A 75 122.46 179.95 REMARK 500 1 LYS A 76 97.06 61.70 REMARK 500 1 ALA A 77 -75.31 -154.99 REMARK 500 1 GLN A 80 -62.01 -156.54 REMARK 500 1 GLN A 81 86.64 60.07 REMARK 500 1 HIS A 82 124.24 -177.08 REMARK 500 1 LEU A 94 44.13 -95.81 REMARK 500 1 GLU A 95 34.04 -94.07 REMARK 500 1 THR A 123 -66.14 -101.51 REMARK 500 1 SER A 143 31.36 -96.55 REMARK 500 2 LYS A 2 -77.96 65.33 REMARK 500 2 THR A 5 53.52 -100.90 REMARK 500 2 LEU A 7 -18.27 76.49 REMARK 500 2 ASP A 20 107.66 -58.14 REMARK 500 2 ASN A 22 31.76 -96.12 REMARK 500 2 ASP A 24 91.41 -56.87 REMARK 500 2 GLU A 26 -83.86 -65.78 REMARK 500 2 PHE A 27 140.70 -173.04 REMARK 500 2 ARG A 39 171.07 -47.64 REMARK 500 2 SER A 41 -113.35 -79.07 REMARK 500 2 CYS A 42 160.46 64.87 REMARK 500 2 ARG A 43 28.40 -160.13 REMARK 500 2 ARG A 45 99.09 -66.17 REMARK 500 2 ALA A 47 110.67 60.26 REMARK 500 2 LEU A 48 -171.86 -68.56 REMARK 500 2 GLU A 50 -40.63 -175.64 REMARK 500 2 GLN A 73 85.17 58.86 REMARK 500 2 ALA A 77 -48.72 -156.25 REMARK 500 2 ASN A 78 91.94 60.31 REMARK 500 3 ASN A 22 32.30 -98.18 REMARK 500 3 ASP A 24 89.80 -57.45 REMARK 500 3 GLU A 26 -87.50 -66.33 REMARK 500 3 PHE A 27 139.35 -170.02 REMARK 500 3 ARG A 39 170.74 -47.58 REMARK 500 3 SER A 41 -124.56 -79.02 REMARK 500 3 CYS A 42 162.40 71.90 REMARK 500 REMARK 500 THIS ENTRY HAS 369 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 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SMC A 38 SG REMARK 620 2 CYS A 42 SG 80.2 REMARK 620 3 CYS A 69 SG 78.9 133.0 REMARK 620 4 CYS A 72 SG 126.4 96.5 129.6 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 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6054 RELATED DB: BMRB REMARK 900 1H, 15N AND 13C RESONANCE ASSIGNMENTS OF THIS PROTEIN. REMARK 900 RELATED ID: 1ADN RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN REMARK 900 OF ESCHERICHIA COLI ADA. REMARK 900 RELATED ID: 1EYF RELATED DB: PDB REMARK 900 REFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN REMARK 900 OF E. COLI ADA. DBREF 1WPK A 1 146 UNP P06134 ADA_ECOLI 1 146 SEQADV 1WPK SMC A 38 UNP P06134 CYS 38 MODIFIED RESIDUE SEQRES 1 A 146 MET LYS LYS ALA THR CYS LEU THR ASP ASP GLN ARG TRP SEQRES 2 A 146 GLN SER VAL LEU ALA ARG ASP PRO ASN ALA ASP GLY GLU SEQRES 3 A 146 PHE VAL PHE ALA VAL ARG THR THR GLY ILE PHE SMC ARG SEQRES 4 A 146 PRO SER CYS ARG ALA ARG HIS ALA LEU ARG GLU ASN VAL SEQRES 5 A 146 SER PHE TYR ALA ASN ALA SER GLU ALA LEU ALA ALA GLY SEQRES 6 A 146 PHE ARG PRO CYS LYS ARG CYS GLN PRO GLU LYS ALA ASN SEQRES 7 A 146 ALA GLN GLN HIS ARG LEU ASP LYS ILE THR HIS ALA CYS SEQRES 8 A 146 ARG LEU LEU GLU GLN GLU THR PRO VAL THR LEU GLU ALA SEQRES 9 A 146 LEU ALA ASP GLN VAL ALA MET SER PRO PHE HIS LEU HIS SEQRES 10 A 146 ARG LEU PHE LYS ALA THR THR GLY MET THR PRO LYS ALA SEQRES 11 A 146 TRP GLN GLN ALA TRP ARG ALA ARG ARG LEU ARG GLU SER SEQRES 12 A 146 LEU ALA LYS MODRES 1WPK SMC A 38 CYS S-METHYLCYSTEINE HET SMC A 38 14 HET ZN A 200 1 HETNAM SMC S-METHYLCYSTEINE HETNAM ZN ZINC ION FORMUL 1 SMC C4 H9 N O2 S FORMUL 2 ZN ZN 2+ HELIX 1 1 THR A 8 ARG A 19 1 12 HELIX 2 2 ASN A 57 PHE A 66 1 10 HELIX 3 3 HIS A 82 LEU A 94 1 13 HELIX 4 4 THR A 101 ALA A 110 1 10 HELIX 5 5 SER A 112 THR A 124 1 13 HELIX 6 6 THR A 127 GLU A 142 1 16 SHEET 1 A 4 VAL A 52 TYR A 55 0 SHEET 2 A 4 VAL A 28 VAL A 31 -1 N ALA A 30 O SER A 53 SHEET 3 A 4 ILE A 36 SMC A 38 -1 O ILE A 36 N VAL A 31 SHEET 4 A 4 ARG A 67 CYS A 69 1 O ARG A 67 N PHE A 37 LINK C PHE A 37 N SMC A 38 1555 1555 1.33 LINK C SMC A 38 N ARG A 39 1555 1555 1.33 LINK SG SMC A 38 ZN ZN A 200 1555 1555 2.64 LINK SG CYS A 42 ZN ZN A 200 1555 1555 2.54 LINK SG CYS A 69 ZN ZN A 200 1555 1555 2.50 LINK SG CYS A 72 ZN ZN A 200 1555 1555 2.52 SITE 1 AC1 5 SMC A 38 CYS A 42 CYS A 69 LYS A 70 SITE 2 AC1 5 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