HEADER TRANSCRIPTION 11-JUN-08 2K4J TITLE ARSR DNA BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN, UNP RESIDUE 123-225; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI J99; SOURCE 4 ORGANISM_TAXID: 85963; SOURCE 5 STRAIN: J99; SOURCE 6 GENE: JHP_0152; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-BNK KEYWDS RESPONSE REGULATOR, HELICOBACTER PYLORI, ACID RESISTANCE, DNA- KEYWDS 2 BINDING, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.S.GUPTA,T.L.COVER,A.M.KREZEL REVDAT 4 14-JUN-23 2K4J 1 REMARK REVDAT 3 19-FEB-20 2K4J 1 REMARK SEQADV REVDAT 2 13-JUL-11 2K4J 1 VERSN REVDAT 1 30-DEC-08 2K4J 0 JRNL AUTH S.S.GUPTA,T.L.COVER,A.M.KREZEL JRNL TITL ARSR DNA BINDING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9, CYANA 2.1 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM (AMBER), GUNTERT, REMARK 3 MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CYANA BASED REFINEMENT, ENERGY REMARK 3 MINIMIZATION WITH AMBER PROGRAM REMARK 4 REMARK 4 2K4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000100666. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.6 REMARK 210 IONIC STRENGTH : 0.56 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 ENTITY, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D CBCANH; 3D HCC-TOCSY; 3D HHC- REMARK 210 TOCSY; 3D H(CC)(CO)NH; 3D HCC(CO) REMARK 210 NH; 3D HBHA(CO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, CSI 2.0, MOLMOL 2K.2, REMARK 210 PROCHECKNMR 3.5.4, PROCHECK REMARK 210 3.5.4, TOPSPIN 2.0, SPARKY 3.114, REMARK 210 INSIGHT II V2005.03 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 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 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 4 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 44 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 11 TYR A 47 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 TYR A 47 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 VAL A 84 CA - CB - CG1 ANGL. DEV. = 9.7 DEGREES REMARK 500 18 PHE A 61 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 18 TYR A 111 CB - CG - CD2 ANGL. DEV. = -3.6 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 16 43.16 -152.94 REMARK 500 1 ASN A 22 -96.86 51.02 REMARK 500 1 ARG A 31 51.78 76.90 REMARK 500 1 LYS A 38 149.61 -172.04 REMARK 500 1 ASP A 41 62.31 -164.89 REMARK 500 1 LEU A 42 -106.58 -84.33 REMARK 500 1 LYS A 56 -70.64 -75.15 REMARK 500 1 LYS A 57 152.11 167.57 REMARK 500 1 TYR A 59 -154.83 59.28 REMARK 500 1 GLN A 101 -30.21 -140.05 REMARK 500 1 ARG A 107 -126.91 47.38 REMARK 500 2 ALA A 21 64.62 -159.03 REMARK 500 2 ASN A 22 -87.93 61.58 REMARK 500 2 ARG A 31 54.02 75.83 REMARK 500 2 ASP A 41 46.72 -160.56 REMARK 500 2 LEU A 42 -110.66 -69.51 REMARK 500 2 LYS A 57 150.09 103.18 REMARK 500 2 TYR A 59 -148.71 58.71 REMARK 500 2 SER A 70 -60.06 -92.39 REMARK 500 2 SER A 72 20.20 -72.81 REMARK 500 2 GLN A 101 -31.29 -152.60 REMARK 500 2 ILE A 109 -60.22 -129.34 REMARK 500 3 ALA A 21 71.48 -156.90 REMARK 500 3 ASN A 22 -93.86 59.43 REMARK 500 3 LYS A 38 162.58 177.01 REMARK 500 3 ASP A 41 50.66 -156.92 REMARK 500 3 LEU A 42 -140.53 -88.33 REMARK 500 3 LYS A 57 147.10 104.64 REMARK 500 3 TYR A 59 -167.59 61.84 REMARK 500 3 GLN A 101 -38.04 -172.00 REMARK 500 4 GLU A 14 -80.86 -108.61 REMARK 500 4 ALA A 21 62.75 -156.95 REMARK 500 4 ASN A 22 -90.20 60.05 REMARK 500 4 ARG A 31 63.25 66.73 REMARK 500 4 ASP A 41 59.12 -165.03 REMARK 500 4 LEU A 42 -123.85 -85.95 REMARK 500 4 LYS A 57 155.83 136.52 REMARK 500 4 TYR A 59 -155.61 58.90 REMARK 500 4 GLU A 71 -11.09 70.02 REMARK 500 4 SER A 72 30.99 -74.40 REMARK 500 4 GLN A 101 -34.34 -156.88 REMARK 500 5 GLU A 14 2.37 -168.08 REMARK 500 5 ASN A 22 -91.36 61.15 REMARK 500 5 LYS A 38 149.62 174.64 REMARK 500 5 LEU A 42 -90.11 -157.39 REMARK 500 5 LYS A 57 151.30 133.13 REMARK 500 5 TYR A 59 -164.06 60.71 REMARK 500 5 GLN A 101 -38.56 -169.07 REMARK 500 6 ALA A 21 71.26 -160.63 REMARK 500 6 ASN A 22 -82.39 59.05 REMARK 500 REMARK 500 THIS ENTRY HAS 165 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 LEU A 40 ASP A 41 11 -147.90 REMARK 500 LEU A 40 ASP A 41 12 -148.20 REMARK 500 SER A 70 GLU A 71 19 146.59 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 6 TYR A 111 0.08 SIDE CHAIN REMARK 500 18 TYR A 111 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15801 RELATED DB: BMRB DBREF 2K4J A 13 115 UNP Q9ZMR6 Q9ZMR6_HELPJ 123 225 SEQADV 2K4J MET A 1 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J ARG A 2 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J GLY A 3 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J SER A 4 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J HIS A 5 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J HIS A 6 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J HIS A 7 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J HIS A 8 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J HIS A 9 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J HIS A 10 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J GLY A 11 UNP Q9ZMR6 EXPRESSION TAG SEQADV 2K4J SER A 12 UNP Q9ZMR6 EXPRESSION TAG SEQRES 1 A 115 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLU SEQRES 2 A 115 GLU VAL SER GLU PRO GLY ASP ALA ASN ILE PHE ARG VAL SEQRES 3 A 115 ASP LYS ASP SER ARG GLU VAL TYR MET HIS GLU LYS LYS SEQRES 4 A 115 LEU ASP LEU THR ARG ALA GLU TYR GLU ILE LEU SER LEU SEQRES 5 A 115 LEU ILE SER LYS LYS GLY TYR VAL PHE SER ARG GLU SER SEQRES 6 A 115 ILE ALA ILE GLU SER GLU SER ILE ASN PRO GLU SER SER SEQRES 7 A 115 ASN LYS SER ILE ASP VAL ILE ILE GLY ARG LEU ARG SER SEQRES 8 A 115 LYS ILE GLU LYS ASN PRO LYS GLN PRO GLN TYR ILE ILE SEQRES 9 A 115 SER VAL ARG GLY ILE GLY TYR LYS LEU GLU TYR HELIX 1 1 THR A 43 LYS A 57 1 15 HELIX 2 2 SER A 62 SER A 70 1 9 HELIX 3 3 SER A 78 ASN A 96 1 19 SHEET 1 A 4 GLY A 19 ALA A 21 0 SHEET 2 A 4 PHE A 24 ASP A 27 -1 O PHE A 24 N ALA A 21 SHEET 3 A 4 GLU A 32 MET A 35 -1 O GLU A 32 N ASP A 27 SHEET 4 A 4 LYS A 38 LEU A 40 -1 O LEU A 40 N VAL A 33 SHEET 1 B 3 VAL A 60 PHE A 61 0 SHEET 2 B 3 GLY A 110 LYS A 112 -1 O TYR A 111 N PHE A 61 SHEET 3 B 3 ILE A 104 VAL A 106 -1 N VAL A 106 O GLY A 110 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