HEADER SIGNALING PROTEIN 19-JUL-06 2HQR TITLE STRUCTURE OF A ATYPICAL ORPHAN RESPONSE REGULATOR PROTEIN REVEALED A TITLE 2 NEW PHOSPHORYLATION-INDEPENDENT REGULATORY MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85963; SOURCE 4 STRAIN: J99; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPORYLATION-INDEPENDENT RESPONSE REGULATOR, H. PYLORI, SYMMETRIC KEYWDS 2 DIMER, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.HONG,W.LEE REVDAT 4 13-JUL-11 2HQR 1 VERSN REVDAT 3 24-FEB-09 2HQR 1 VERSN REVDAT 2 24-JUL-07 2HQR 1 JRNL REVDAT 1 08-MAY-07 2HQR 0 JRNL AUTH E.HONG,H.M.LEE,H.KO,D.-U.KIM,B.-Y.JEON,J.JUNG,J.SHIN, JRNL AUTH 2 S.-A.LEE,Y.KIM,Y.H.JEON,C.CHEONG,H.-S.CHO,W.LEE JRNL TITL STRUCTURE OF AN ATYPICAL ORPHAN RESPONSE REGULATOR PROTEIN JRNL TITL 2 SUPPORTS A NEW PHOSPHORYLATION-INDEPENDENT REGULATORY JRNL TITL 3 MECHANISM JRNL REF J.BIOL.CHEM. V. 282 20667 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17491010 JRNL DOI 10.1074/JBC.M609104200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1 REMARK 3 AUTHORS : GUENTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HQR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-06. REMARK 100 THE RCSB ID CODE IS RCSB038650. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.23 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50MM KH2PO4; 300MM KCL; 2MM DTT; REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, NMRPIPE 2.4, SPARKY REMARK 210 3.112 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 3D HETERONUCLEAR REMARK 210 TECHNIQUES. 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 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 HH12 ARG B 192 HG22 VAL B 204 1.12 REMARK 500 HH12 ARG B 192 CG2 VAL B 204 1.17 REMARK 500 HH11 ARG B 192 HG22 VAL B 204 1.21 REMARK 500 HH12 ARG B 192 CB VAL B 204 1.22 REMARK 500 NH1 ARG B 192 HG22 VAL B 204 1.26 REMARK 500 HH12 ARG B 192 HB VAL B 204 1.31 REMARK 500 HH22 ARG B 192 HB VAL B 204 1.32 REMARK 500 O ARG A 61 H LYS A 65 1.47 REMARK 500 O ARG B 157 H ARG B 159 1.52 REMARK 500 O GLY A 146 HD1 PHE A 149 1.52 REMARK 500 O GLU B 81 HD1 HIS B 85 1.55 REMARK 500 O SER B 101 H LYS B 103 1.56 REMARK 500 O LEU B 33 H GLU B 37 1.57 REMARK 500 H ASN A 182 H VAL A 183 1.57 REMARK 500 O GLN A 193 HZ3 LYS A 197 1.58 REMARK 500 HZ1 LYS A 53 OD1 ASP A 76 1.58 REMARK 500 O ARG A 100 HG SER A 101 1.59 REMARK 500 NH1 ARG B 192 CG2 VAL B 204 1.90 REMARK 500 NH1 ARG B 192 CB VAL B 204 2.16 REMARK 500 O SER B 101 N LYS B 103 2.18 REMARK 500 NZ LYS B 138 O PRO B 198 2.18 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 31 -102.92 -87.41 REMARK 500 1 HIS A 66 70.90 -157.69 REMARK 500 1 SER A 68 49.87 -90.83 REMARK 500 1 SER A 75 121.84 -171.20 REMARK 500 1 PRO A 78 81.38 -66.92 REMARK 500 1 PRO A 98 -12.50 -39.55 REMARK 500 1 TYR A 99 131.09 59.86 REMARK 500 1 SER A 101 43.82 -174.42 REMARK 500 1 ILE A 102 -80.26 47.47 REMARK 500 1 ARG A 114 -77.66 -85.64 REMARK 500 1 TRP A 116 97.69 49.85 REMARK 500 1 GLU A 133 72.71 55.00 REMARK 500 1 LYS A 145 28.76 -154.34 REMARK 500 1 TRP A 173 74.73 -108.88 REMARK 500 1 PRO A 176 109.60 -42.87 REMARK 500 1 MET A 178 70.14 -64.44 REMARK 500 1 THR A 180 92.22 47.73 REMARK 500 1 PRO A 181 76.73 -47.37 REMARK 500 1 ASN A 182 -20.22 -174.01 REMARK 500 1 ARG A 210 -78.55 57.68 REMARK 500 1 PRO A 217 151.94 -39.45 REMARK 500 1 GLU B 31 -107.34 -93.21 REMARK 500 1 HIS B 66 64.50 -155.28 REMARK 500 1 SER B 68 47.56 -70.18 REMARK 500 1 SER B 75 125.07 -172.49 REMARK 500 1 ASP B 76 21.57 -76.04 REMARK 500 1 ASN B 77 58.77 -146.75 REMARK 500 1 PRO B 78 83.30 -57.96 REMARK 500 1 PRO B 98 -10.35 -40.44 REMARK 500 1 TYR B 99 118.70 59.03 REMARK 500 1 SER B 101 44.84 -173.87 REMARK 500 1 ILE B 102 -69.90 49.25 REMARK 500 1 ARG B 114 -73.25 -90.65 REMARK 500 1 TRP B 116 84.87 52.01 REMARK 500 1 LYS B 145 70.17 -176.18 REMARK 500 1 HIS B 158 48.08 -67.97 REMARK 500 1 ILE B 172 -80.91 -133.06 REMARK 500 1 TRP B 173 173.99 152.61 REMARK 500 1 GLU B 174 -59.55 -165.28 REMARK 500 1 MET B 178 28.64 49.35 REMARK 500 1 PRO B 181 158.47 -42.27 REMARK 500 1 THR B 203 20.80 -149.89 REMARK 500 1 ARG B 210 -50.55 -148.44 REMARK 500 1 PRO B 217 -169.53 -66.73 REMARK 500 1 LYS B 218 153.39 -47.68 REMARK 500 1 PRO B 219 102.10 -38.05 REMARK 500 2 GLU A 31 -106.37 -93.09 REMARK 500 2 ASP A 46 -38.70 -132.34 REMARK 500 2 HIS A 66 64.96 -152.66 REMARK 500 2 PRO A 78 83.83 -50.97 REMARK 500 REMARK 500 THIS ENTRY HAS 934 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HQN RELATED DB: PDB REMARK 900 THE C-TERMINAL DOMAIN OF THE SAME PROTEIN IN MONOMER FORM REMARK 900 RELATED ID: 2HQO RELATED DB: PDB REMARK 900 THE N-TERMINAL DOMAIN OF THE SAME PROTEIN IN DIMER FORM DBREF 2HQR A 1 223 UNP Q9ZM42 Q9ZM42_HELPJ 1 223 DBREF 2HQR B 1 223 UNP Q9ZM42 Q9ZM42_HELPJ 1 223 SEQRES 1 A 223 MET ARG VAL LEU LEU ILE GLU LYS ASN SER VAL LEU GLY SEQRES 2 A 223 GLY GLU ILE GLU LYS GLY LEU ASN VAL LYS GLY PHE MET SEQRES 3 A 223 ALA ASP VAL THR GLU SER LEU GLU ASP GLY GLU TYR LEU SEQRES 4 A 223 MET ASP ILE ARG ASN TYR ASP LEU VAL MET VAL SER ASP SEQRES 5 A 223 LYS ASN ALA LEU SER PHE VAL SER ARG ILE LYS GLU LYS SEQRES 6 A 223 HIS SER SER ILE VAL VAL LEU VAL SER SER ASP ASN PRO SEQRES 7 A 223 THR SER GLU GLU GLU VAL HIS ALA PHE GLU GLN GLY ALA SEQRES 8 A 223 ASP ASP TYR ILE ALA LYS PRO TYR ARG SER ILE LYS ALA SEQRES 9 A 223 LEU VAL ALA ARG ILE GLU ALA ARG LEU ARG PHE TRP GLY SEQRES 10 A 223 SER ASN VAL ILE GLU ILE GLY ASP LEU THR ILE SER PRO SEQRES 11 A 223 ASP GLU GLU LYS ILE ILE TYR LYS GLY ARG GLU VAL GLU SEQRES 12 A 223 VAL LYS GLY LYS PRO PHE GLU VAL LEU THR HIS LEU ALA SEQRES 13 A 223 ARG HIS ARG ASP GLN ILE VAL SER LYS GLU GLN LEU LEU SEQRES 14 A 223 ASP ALA ILE TRP GLU GLU PRO GLU MET VAL THR PRO ASN SEQRES 15 A 223 VAL ILE GLU VAL ALA ILE ASN GLN ILE ARG GLN LYS MET SEQRES 16 A 223 ASP LYS PRO LEU GLY ILE SER THR VAL GLU THR VAL ARG SEQRES 17 A 223 ARG ARG GLY TYR ARG PHE CYS TYR PRO LYS PRO ALA CYS SEQRES 18 A 223 GLU GLU SEQRES 1 B 223 MET ARG VAL LEU LEU ILE GLU LYS ASN SER VAL LEU GLY SEQRES 2 B 223 GLY GLU ILE GLU LYS GLY LEU ASN VAL LYS GLY PHE MET SEQRES 3 B 223 ALA ASP VAL THR GLU SER LEU GLU ASP GLY GLU TYR LEU SEQRES 4 B 223 MET ASP ILE ARG ASN TYR ASP LEU VAL MET VAL SER ASP SEQRES 5 B 223 LYS ASN ALA LEU SER PHE VAL SER ARG ILE LYS GLU LYS SEQRES 6 B 223 HIS SER SER ILE VAL VAL LEU VAL SER SER ASP ASN PRO SEQRES 7 B 223 THR SER GLU GLU GLU VAL HIS ALA PHE GLU GLN GLY ALA SEQRES 8 B 223 ASP ASP TYR ILE ALA LYS PRO TYR ARG SER ILE LYS ALA SEQRES 9 B 223 LEU VAL ALA ARG ILE GLU ALA ARG LEU ARG PHE TRP GLY SEQRES 10 B 223 SER ASN VAL ILE GLU ILE GLY ASP LEU THR ILE SER PRO SEQRES 11 B 223 ASP GLU GLU LYS ILE ILE TYR LYS GLY ARG GLU VAL GLU SEQRES 12 B 223 VAL LYS GLY LYS PRO PHE GLU VAL LEU THR HIS LEU ALA SEQRES 13 B 223 ARG HIS ARG ASP GLN ILE VAL SER LYS GLU GLN LEU LEU SEQRES 14 B 223 ASP ALA ILE TRP GLU GLU PRO GLU MET VAL THR PRO ASN SEQRES 15 B 223 VAL ILE GLU VAL ALA ILE ASN GLN ILE ARG GLN LYS MET SEQRES 16 B 223 ASP LYS PRO LEU GLY ILE SER THR VAL GLU THR VAL ARG SEQRES 17 B 223 ARG ARG GLY TYR ARG PHE CYS TYR PRO LYS PRO ALA CYS SEQRES 18 B 223 GLU GLU HELIX 1 1 ASN A 9 ASN A 21 1 13 HELIX 2 2 VAL A 22 GLY A 24 5 3 HELIX 3 3 SER A 32 ASP A 41 1 10 HELIX 4 4 ASN A 54 HIS A 66 1 13 HELIX 5 5 THR A 79 GLY A 90 1 12 HELIX 6 6 ILE A 102 LEU A 113 1 12 HELIX 7 7 PHE A 149 HIS A 158 1 10 HELIX 8 8 LYS A 165 TRP A 173 1 9 HELIX 9 9 VAL A 179 ASN A 182 5 4 HELIX 10 10 VAL A 183 LYS A 197 1 15 HELIX 11 11 PRO A 217 CYS A 221 5 5 HELIX 12 12 ASN B 9 ASN B 21 1 13 HELIX 13 13 VAL B 22 GLY B 24 5 3 HELIX 14 14 SER B 32 ARG B 43 1 12 HELIX 15 15 ASN B 54 HIS B 66 1 13 HELIX 16 16 THR B 79 GLY B 90 1 12 HELIX 17 17 ILE B 102 LEU B 113 1 12 HELIX 18 18 GLY B 146 HIS B 158 1 13 HELIX 19 19 SER B 164 ILE B 172 1 9 HELIX 20 20 ASN B 182 GLY B 200 1 19 SHEET 1 A 5 ALA A 27 THR A 30 0 SHEET 2 A 5 VAL A 3 ILE A 6 1 N LEU A 5 O ASP A 28 SHEET 3 A 5 LEU A 47 VAL A 50 1 O LEU A 47 N LEU A 4 SHEET 4 A 5 VAL A 70 SER A 75 1 O SER A 74 N VAL A 50 SHEET 5 A 5 ASP A 93 ALA A 96 1 O ILE A 95 N VAL A 73 SHEET 1 B 4 ILE A 121 ILE A 123 0 SHEET 2 B 4 LEU A 126 SER A 129 -1 O LEU A 126 N ILE A 123 SHEET 3 B 4 LYS A 134 TYR A 137 -1 O LYS A 134 N SER A 129 SHEET 4 B 4 ARG A 140 VAL A 142 -1 O VAL A 142 N ILE A 135 SHEET 1 C 3 GLN A 161 SER A 164 0 SHEET 2 C 3 GLY A 211 PHE A 214 -1 O PHE A 214 N GLN A 161 SHEET 3 C 3 VAL A 204 THR A 206 -1 N GLU A 205 O ARG A 213 SHEET 1 D 5 MET B 26 THR B 30 0 SHEET 2 D 5 ARG B 2 ILE B 6 1 N VAL B 3 O MET B 26 SHEET 3 D 5 LEU B 47 VAL B 50 1 O LEU B 47 N LEU B 4 SHEET 4 D 5 VAL B 70 SER B 75 1 O LEU B 72 N VAL B 48 SHEET 5 D 5 ASP B 93 ALA B 96 1 O ILE B 95 N VAL B 73 SHEET 1 E 4 ILE B 121 ILE B 123 0 SHEET 2 E 4 LEU B 126 SER B 129 -1 O LEU B 126 N ILE B 123 SHEET 3 E 4 LYS B 134 TYR B 137 -1 O LYS B 134 N SER B 129 SHEET 4 E 4 ARG B 140 GLU B 143 -1 O ARG B 140 N TYR B 137 SHEET 1 F 3 GLN B 161 VAL B 163 0 SHEET 2 F 3 TYR B 212 PHE B 214 -1 O TYR B 212 N VAL B 163 SHEET 3 F 3 VAL B 204 THR B 206 -1 N GLU B 205 O ARG B 213 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