HEADER HYDROLASE 25-NOV-12 2M1C TITLE HADDOCK STRUCTURE OF GTYYBT PAS HOMODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DHH SUBFAMILY 1 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 420246; SOURCE 4 STRAIN: NG80-2; SOURCE 5 GENE: DHH SUBFAMILY 1, GTNG_3419; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET26 KEYWDS PAS DOMAIN, YYBT, LIGAND BINDING, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR Z.X.LIANG,K.PERVUSHIN,E.TAN,F.RAO,S.PASUNOOTI,I.SOEHANO,J.LESCAR REVDAT 3 14-JUN-23 2M1C 1 SEQADV REVDAT 2 22-MAY-13 2M1C 1 JRNL REVDAT 1 27-MAR-13 2M1C 0 JRNL AUTH E.TAN,F.RAO,S.PASUNOOTI,T.H.PHAM,I.SOEHANO,M.S.TURNER, JRNL AUTH 2 C.W.LIEW,J.LESCAR,K.PERVUSHIN,Z.X.LIANG JRNL TITL SOLUTION STRUCTURE OF THE PAS DOMAIN OF A THERMOPHILIC YYBT JRNL TITL 2 PROTEIN HOMOLOG REVEALS A POTENTIAL LIGAND-BINDING SITE. JRNL REF J.BIOL.CHEM. V. 288 11949 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23504327 JRNL DOI 10.1074/JBC.M112.437764 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, HADDOCK REMARK 3 AUTHORS : BRUNGER A.T. ET.AL. (CNS), ALEXANDRE BONVIN REMARK 3 (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: H2O SOLVATED DOCKING REMARK 4 REMARK 4 2M1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000103084. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 50MM NAP, PH 6.5, 200MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-99% 13C; U-99% 15N] REMARK 210 PAS DOMAIN OF DHH SUBFAMILY 1 REMARK 210 PROTEIN, 50MM PHOSPHATE BUFFER REMARK 210 NA; 95% H2O, 5% D2O, PH 6.5, REMARK 210 200MM NACL, 1X PROTEASE INHIBITOR REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D_15N_TROSY-HSQC; 2D_13C_HMQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCO; REMARK 210 3D_HN(CA)CO; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D_15N-SEPARATED_NOESY; REMARK 210 3D_13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : TOP 4 STRUCTURES FROM HADDOCK REMARK 210 WEBSERVER 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 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 OE1 GLU A 134 HZ3 LYS B 145 1.52 REMARK 500 HZ3 LYS B 142 OD2 ASP B 159 1.57 REMARK 500 HZ3 LYS A 145 OE1 GLU B 134 1.60 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 HIS A 57 -69.07 70.24 REMARK 500 1 ILE A 64 44.36 -80.61 REMARK 500 1 SER A 65 -70.36 -104.79 REMARK 500 1 VAL A 71 52.86 36.74 REMARK 500 1 LYS A 73 -16.85 75.13 REMARK 500 1 ALA A 78 174.44 76.13 REMARK 500 1 GLN A 81 -20.60 -171.09 REMARK 500 1 ASP A 90 -151.72 -90.07 REMARK 500 1 ASP A 93 18.45 124.37 REMARK 500 1 SER A 115 -158.18 49.26 REMARK 500 1 LYS A 131 55.08 -103.75 REMARK 500 1 THR A 132 -177.05 -172.63 REMARK 500 1 ASP A 133 -73.89 -109.55 REMARK 500 1 HIS A 149 -142.25 -124.41 REMARK 500 1 ARG A 150 -105.51 -68.07 REMARK 500 1 HIS A 151 24.70 -54.79 REMARK 500 1 GLU A 152 43.79 1.24 REMARK 500 1 HIS B 57 -63.69 72.57 REMARK 500 1 ILE B 64 42.18 -75.69 REMARK 500 1 SER B 65 -71.58 -99.84 REMARK 500 1 VAL B 71 60.39 36.61 REMARK 500 1 LYS B 73 -12.96 68.19 REMARK 500 1 ALA B 78 168.77 73.71 REMARK 500 1 GLN B 81 -20.11 -170.97 REMARK 500 1 ASP B 90 -153.86 -89.41 REMARK 500 1 ASP B 93 19.91 123.03 REMARK 500 1 PHE B 101 -39.11 -37.42 REMARK 500 1 SER B 115 -161.24 49.99 REMARK 500 1 LYS B 131 59.43 -96.20 REMARK 500 1 THR B 132 -177.22 -173.44 REMARK 500 1 ASP B 133 -74.09 -111.77 REMARK 500 1 HIS B 149 -146.82 -125.45 REMARK 500 1 ARG B 150 -104.91 -63.51 REMARK 500 1 HIS B 151 27.94 -53.58 REMARK 500 1 GLU B 152 40.89 3.59 REMARK 500 2 HIS A 57 -50.36 69.84 REMARK 500 2 LYS A 73 -17.04 70.70 REMARK 500 2 ALA A 78 107.08 71.14 REMARK 500 2 GLN A 81 -22.69 -165.67 REMARK 500 2 ILE A 84 38.97 -92.42 REMARK 500 2 ASP A 90 -142.97 -90.72 REMARK 500 2 ASP A 93 44.32 112.92 REMARK 500 2 GLU A 96 -64.45 -96.28 REMARK 500 2 LYS A 107 68.00 70.36 REMARK 500 2 SER A 115 -172.11 52.30 REMARK 500 2 THR A 132 -176.50 -174.33 REMARK 500 2 ASP A 133 -69.13 -100.98 REMARK 500 2 ASN A 140 16.42 59.19 REMARK 500 2 HIS A 149 -122.87 -131.31 REMARK 500 2 ARG A 150 -117.40 -103.96 REMARK 500 REMARK 500 THIS ENTRY HAS 141 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 ARG B 150 10.01 REMARK 500 2 ARG A 150 10.20 REMARK 500 2 ARG B 150 11.11 REMARK 500 3 ARG A 150 15.33 REMARK 500 3 ARG B 150 13.21 REMARK 500 4 SER A 75 11.70 REMARK 500 4 GLU A 92 -21.16 REMARK 500 4 ARG A 150 -13.44 REMARK 500 4 HIS A 151 -10.73 REMARK 500 4 LEU A 154 10.63 REMARK 500 4 SER B 75 10.62 REMARK 500 4 GLU B 92 -21.46 REMARK 500 4 ARG B 150 -13.59 REMARK 500 4 LEU B 154 10.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18856 RELATED DB: BMRB DBREF 2M1C A 54 161 UNP A4ITV2 A4ITV2_GEOTN 55 162 DBREF 2M1C B 54 161 UNP A4ITV2 A4ITV2_GEOTN 55 162 SEQADV 2M1C ARG A 49 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C GLY A 50 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C SER A 51 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C HIS A 52 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C MET A 53 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C ARG B 49 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C GLY B 50 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C SER B 51 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C HIS B 52 UNP A4ITV2 EXPRESSION TAG SEQADV 2M1C MET B 53 UNP A4ITV2 EXPRESSION TAG SEQRES 1 A 113 ARG GLY SER HIS MET ARG SER LEU HIS LYS GLU LEU GLN SEQRES 2 A 113 GLN TYR ILE SER ASN LEU SER TYR ARG VAL LYS LYS VAL SEQRES 3 A 113 SER GLU GLU ALA LEU MET GLN MET PRO ILE GLY ILE LEU SEQRES 4 A 113 LEU LEU ASP GLU GLU ASP LYS ILE GLU TRP SER ASN ARG SEQRES 5 A 113 PHE LEU ALA ALA CYS PHE LYS GLU GLN THR LEU ILE GLY SEQRES 6 A 113 ARG SER LEU ALA GLU LEU SER GLU PRO LEU ALA ALA PHE SEQRES 7 A 113 VAL LYS LYS GLY LYS THR ASP GLU GLU ILE ILE GLU LEU SEQRES 8 A 113 ASN GLY LYS GLN LEU LYS VAL ILE VAL HIS ARG HIS GLU SEQRES 9 A 113 ARG LEU LEU TYR PHE PHE ASP VAL THR SEQRES 1 B 113 ARG GLY SER HIS MET ARG SER LEU HIS LYS GLU LEU GLN SEQRES 2 B 113 GLN TYR ILE SER ASN LEU SER TYR ARG VAL LYS LYS VAL SEQRES 3 B 113 SER GLU GLU ALA LEU MET GLN MET PRO ILE GLY ILE LEU SEQRES 4 B 113 LEU LEU ASP GLU GLU ASP LYS ILE GLU TRP SER ASN ARG SEQRES 5 B 113 PHE LEU ALA ALA CYS PHE LYS GLU GLN THR LEU ILE GLY SEQRES 6 B 113 ARG SER LEU ALA GLU LEU SER GLU PRO LEU ALA ALA PHE SEQRES 7 B 113 VAL LYS LYS GLY LYS THR ASP GLU GLU ILE ILE GLU LEU SEQRES 8 B 113 ASN GLY LYS GLN LEU LYS VAL ILE VAL HIS ARG HIS GLU SEQRES 9 B 113 ARG LEU LEU TYR PHE PHE ASP VAL THR HELIX 1 1 HIS A 52 HIS A 57 1 6 HELIX 2 2 HIS A 57 ILE A 64 1 8 HELIX 3 3 ARG A 100 CYS A 105 1 6 HELIX 4 4 GLU A 121 VAL A 127 1 7 HELIX 5 5 HIS B 52 HIS B 57 1 6 HELIX 6 6 HIS B 57 ILE B 64 1 8 HELIX 7 7 ARG B 100 CYS B 105 1 6 HELIX 8 8 GLU B 121 VAL B 127 1 7 SHEET 1 A 5 ILE A 95 SER A 98 0 SHEET 2 A 5 ILE A 86 LEU A 89 -1 N LEU A 88 O TRP A 97 SHEET 3 A 5 TYR A 156 VAL A 160 -1 O PHE A 157 N LEU A 87 SHEET 4 A 5 LYS A 142 ILE A 147 -1 N LYS A 145 O PHE A 158 SHEET 5 A 5 GLU A 134 LEU A 139 -1 N LEU A 139 O LYS A 142 SHEET 1 B 5 ILE B 95 ASN B 99 0 SHEET 2 B 5 ILE B 86 LEU B 89 -1 N LEU B 88 O TRP B 97 SHEET 3 B 5 TYR B 156 VAL B 160 -1 O PHE B 157 N LEU B 87 SHEET 4 B 5 LYS B 142 ILE B 147 -1 N GLN B 143 O VAL B 160 SHEET 5 B 5 GLU B 134 LEU B 139 -1 N LEU B 139 O LYS B 142 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