HEADER GENE REGULATION 11-MAR-08 2K1O TITLE NMR STRUCTURE OF HELICOBACTER PYLORI JHP0511 (HP0564). COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI J99; SOURCE 4 STRAIN: J99; SOURCE 5 GENE: JHP0511; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETBNK KEYWDS HELICOBACTER PYLORI, REPRESSOR, TRANSCRIPTIONAL REGULATOR, DNA- KEYWDS 2 BINDING, RIBBON-HELIX-HELIX, HP0564, JHP0511, UNKNOWN FUNCTION, GENE KEYWDS 3 REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.N.BORIN,A.M.KREZEL REVDAT 3 13-JUL-11 2K1O 1 VERSN REVDAT 2 24-FEB-09 2K1O 1 VERSN REVDAT 1 07-OCT-08 2K1O 0 JRNL AUTH B.N.BORIN,A.M.KREZEL JRNL TITL STRUCTURE OF HP0564 FROM HELICOBACTER PYLORI IDENTIFIES IT JRNL TITL 2 AS A NEW TRANSCRIPTIONAL REGULATOR. JRNL REF PROTEINS V. 73 265 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18623065 JRNL DOI 10.1002/PROT.22159 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CYANA CALCULATIONS, 25000 STEPS, 10000 REMARK 3 STEPS OF CONJUGATE GRADIENT ENERGY MINIMIZATION USING AMBER REMARK 4 REMARK 4 2K1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-08. REMARK 100 THE RCSB ID CODE IS RCSB100563. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM JHP0511, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 1 MM REMARK 210 [U-15N] JHP0511, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 1 MM REMARK 210 [U-13C; U-15N] JHP0511, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 3D CBCA(CO)NH; 3D REMARK 210 C(CO)NH; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, SPARKY, CYANA 2.1, REMARK 210 AMBER 9, PROCHECKNMR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON- REMARK 210 BOND 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 9 REMARK 465 ARG A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 MET B 9 REMARK 465 ARG B 10 REMARK 465 GLY B 11 REMARK 465 SER B 12 REMARK 465 HIS B 13 REMARK 465 HIS B 14 REMARK 465 HIS B 15 REMARK 465 HIS B 16 REMARK 465 HIS B 17 REMARK 465 HIS B 18 REMARK 465 GLY B 19 REMARK 465 SER B 20 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 39 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG B 39 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 14 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 16 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 16 ARG B 40 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 19 ARG B 39 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 20 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG B 55 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 GLU A 45 -42.40 -142.58 REMARK 500 1 GLU A 47 47.72 -67.55 REMARK 500 1 GLU B 45 -45.72 -142.47 REMARK 500 1 SER B 48 91.66 -66.51 REMARK 500 1 LYS B 64 41.19 -144.33 REMARK 500 1 ASN B 68 45.35 -142.60 REMARK 500 2 ARG A 22 36.80 -142.21 REMARK 500 2 GLU A 45 -54.46 -139.91 REMARK 500 2 SER A 48 92.50 -57.77 REMARK 500 2 GLN A 69 36.83 -140.15 REMARK 500 2 ASP A 70 108.98 -54.94 REMARK 500 2 GLU B 45 -10.39 -154.16 REMARK 500 2 ASN B 68 15.52 -141.60 REMARK 500 2 SER B 71 10.87 -145.29 REMARK 500 3 GLU A 45 -11.68 -154.08 REMARK 500 3 VAL A 46 -30.22 -136.55 REMARK 500 3 TYR A 63 58.29 -90.39 REMARK 500 3 SER A 71 109.79 -162.26 REMARK 500 3 GLU B 45 -27.30 -142.06 REMARK 500 4 GLU A 45 -9.61 -151.71 REMARK 500 4 VAL A 46 -33.07 -136.46 REMARK 500 4 LYS A 64 26.44 -68.55 REMARK 500 4 SER A 71 65.80 -159.16 REMARK 500 4 GLU B 45 -30.74 -154.26 REMARK 500 4 SER B 48 91.25 -68.02 REMARK 500 5 GLU A 45 -37.77 -152.99 REMARK 500 5 THR A 60 -34.60 -140.71 REMARK 500 5 GLU B 45 -7.89 -150.74 REMARK 500 5 GLU B 47 -2.33 68.36 REMARK 500 6 GLU A 45 -41.40 -136.83 REMARK 500 6 VAL A 46 -0.42 -143.54 REMARK 500 6 GLU A 47 -22.83 72.10 REMARK 500 6 LYS A 64 8.00 -69.38 REMARK 500 6 ASP A 70 24.47 -143.95 REMARK 500 6 SER A 71 36.58 -146.68 REMARK 500 6 GLU B 45 -53.29 -140.86 REMARK 500 6 SER B 48 86.66 -63.60 REMARK 500 6 LYS B 64 115.94 -161.14 REMARK 500 6 LYS B 65 19.45 -143.07 REMARK 500 6 SER B 71 17.97 -144.78 REMARK 500 7 GLU A 45 -27.60 -162.77 REMARK 500 7 ILE A 61 -63.67 -105.94 REMARK 500 7 SER A 71 13.82 -143.68 REMARK 500 7 GLU B 45 -35.90 -140.13 REMARK 500 7 SER B 48 96.03 -69.44 REMARK 500 7 SER B 72 47.29 -81.29 REMARK 500 8 GLU A 45 -43.79 -137.40 REMARK 500 8 VAL A 46 109.94 -168.58 REMARK 500 8 SER A 48 93.87 -56.96 REMARK 500 8 GLU B 45 -22.00 -151.93 REMARK 500 REMARK 500 THIS ENTRY HAS 114 RAMACHANDRAN OUTLIERS. 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 20 ARG A 39 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15761 RELATED DB: BMRB DBREF 2K1O A 21 74 UNP Q9ZLR7 Q9ZLR7_HELPJ 21 74 DBREF 2K1O B 21 74 UNP Q9ZLR7 Q9ZLR7_HELPJ 21 74 SEQADV 2K1O MET A 9 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O ARG A 10 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O GLY A 11 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O SER A 12 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS A 13 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS A 14 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS A 15 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS A 16 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS A 17 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS A 18 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O GLY A 19 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O SER A 20 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O MET B 9 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O ARG B 10 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O GLY B 11 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O SER B 12 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS B 13 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS B 14 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS B 15 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS B 16 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS B 17 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O HIS B 18 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O GLY B 19 UNP Q9ZLR7 EXPRESSION TAG SEQADV 2K1O SER B 20 UNP Q9ZLR7 EXPRESSION TAG SEQRES 1 A 66 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LYS SEQRES 2 A 66 ARG ASN PHE SER VAL THR PHE TYR LEU SER LYS GLU GLU SEQRES 3 A 66 HIS ASP VAL LEU ARG ARG LEU ALA ASP GLU GLU VAL GLU SEQRES 4 A 66 SER VAL ASN SER PHE VAL LYS ARG HIS ILE LEU LYS THR SEQRES 5 A 66 ILE ILE TYR LYS LYS GLY THR ASN GLN ASP SER SER ILE SEQRES 6 A 66 ASN SEQRES 1 B 66 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LYS SEQRES 2 B 66 ARG ASN PHE SER VAL THR PHE TYR LEU SER LYS GLU GLU SEQRES 3 B 66 HIS ASP VAL LEU ARG ARG LEU ALA ASP GLU GLU VAL GLU SEQRES 4 B 66 SER VAL ASN SER PHE VAL LYS ARG HIS ILE LEU LYS THR SEQRES 5 B 66 ILE ILE TYR LYS LYS GLY THR ASN GLN ASP SER SER ILE SEQRES 6 B 66 ASN HELIX 1 1 LYS A 32 GLU A 44 1 13 HELIX 2 2 SER A 48 ILE A 62 1 15 HELIX 3 3 SER B 31 GLU B 44 1 14 HELIX 4 4 SER B 48 ILE B 62 1 15 SHEET 1 A 2 PHE A 24 SER A 31 0 SHEET 2 A 2 ASN B 23 LEU B 30 -1 O PHE B 24 N LEU A 30 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