HEADER LYASE 27-DEC-19 6VDG TITLE CRYSTAL STRUCTURE OF THE Y182A HISF MUTANT FROM THERMOTOGA MARITIMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IGP SYNTHASE CYCLASE SUBUNIT,IGP SYNTHASE SUBUNIT HISF,IMGP COMPND 5 SYNTHASE SUBUNIT HISF,IGPS SUBUNIT HISF; COMPND 6 EC: 4.3.2.10; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: HISF, TM_1036; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLASE, HISTIDINE PATHWAY, TIM-BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR V.M.ALMEIDA,B.Y.MATSUYAMA,C.S.FARAH,S.R.MARANA REVDAT 3 11-OCT-23 6VDG 1 REMARK REVDAT 2 19-JAN-22 6VDG 1 JRNL REVDAT 1 15-JAN-20 6VDG 0 JRNL AUTH V.MEDEIROS ALMEIDA,A.CHAUDHURI,M.V.CANGUSSU CARDOSO, JRNL AUTH 2 B.Y.MATSUYAMA,G.MONTEIRO FERREIRA,G.H.GOULART TROSSINI, JRNL AUTH 3 R.K.SALINAS,J.P.LORIA,S.R.MARANA JRNL TITL ROLE OF A HIGH CENTRALITY RESIDUE IN PROTEIN DYNAMICS AND JRNL TITL 2 THERMAL STABILITY. JRNL REF J.STRUCT.BIOL. V. 213 07773 2021 JRNL REFN ESSN 1095-8657 JRNL PMID 34320379 JRNL DOI 10.1016/J.JSB.2021.107773 REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 10863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 5.5700 - 4.4300 0.99 1246 140 0.1768 0.2313 REMARK 3 2 4.4300 - 3.8700 0.99 1233 136 0.1754 0.2304 REMARK 3 3 3.8700 - 3.5100 1.00 1219 136 0.2057 0.3077 REMARK 3 4 3.5100 - 3.2600 1.00 1219 136 0.2291 0.2902 REMARK 3 5 3.2600 - 3.0700 1.00 1203 133 0.2229 0.3201 REMARK 3 6 3.0700 - 2.9200 1.00 1208 134 0.2553 0.3515 REMARK 3 7 2.9200 - 2.7900 0.93 1116 124 0.2662 0.3563 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.388 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1864 REMARK 3 ANGLE : 0.730 2518 REMARK 3 CHIRALITY : 0.051 297 REMARK 3 PLANARITY : 0.003 323 REMARK 3 DIHEDRAL : 26.661 689 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000244598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.45851 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10873 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 47.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1GPW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3350, 20MM POTASSIUM REMARK 280 PHOSPHATE, PH 8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.63767 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 103.27533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.45650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 129.09417 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.81883 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.63767 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 103.27533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 129.09417 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.45650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.81883 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 LYS A 19 REMARK 465 GLY A 20 REMARK 465 SER A 21 REMARK 465 ASN A 22 REMARK 465 PHE A 23 REMARK 465 GLU A 24 REMARK 465 ASN A 25 REMARK 465 LEU A 26 REMARK 465 ARG A 27 REMARK 465 ASP A 28 REMARK 465 SER A 29 REMARK 465 GLU A 251 REMARK 465 GLY A 252 REMARK 465 LEU A 253 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 301 DBREF 6VDG A 1 253 UNP Q9X0C6 HIS6_THEMA 1 253 SEQADV 6VDG SER A 21 UNP Q9X0C6 THR 21 CONFLICT SEQADV 6VDG ALA A 182 UNP Q9X0C6 TYR 182 ENGINEERED MUTATION SEQRES 1 A 253 MET LEU ALA LYS ARG ILE ILE ALA CYS LEU ASP VAL LYS SEQRES 2 A 253 ASP GLY ARG VAL VAL LYS GLY SER ASN PHE GLU ASN LEU SEQRES 3 A 253 ARG ASP SER GLY ASP PRO VAL GLU LEU GLY LYS PHE TYR SEQRES 4 A 253 SER GLU ILE GLY ILE ASP GLU LEU VAL PHE LEU ASP ILE SEQRES 5 A 253 THR ALA SER VAL GLU LYS ARG LYS THR MET LEU GLU LEU SEQRES 6 A 253 VAL GLU LYS VAL ALA GLU GLN ILE ASP ILE PRO PHE THR SEQRES 7 A 253 VAL GLY GLY GLY ILE HIS ASP PHE GLU THR ALA SER GLU SEQRES 8 A 253 LEU ILE LEU ARG GLY ALA ASP LYS VAL SER ILE ASN THR SEQRES 9 A 253 ALA ALA VAL GLU ASN PRO SER LEU ILE THR GLN ILE ALA SEQRES 10 A 253 GLN THR PHE GLY SER GLN ALA VAL VAL VAL ALA ILE ASP SEQRES 11 A 253 ALA LYS ARG VAL ASP GLY GLU PHE MET VAL PHE THR TYR SEQRES 12 A 253 SER GLY LYS LYS ASN THR GLY ILE LEU LEU ARG ASP TRP SEQRES 13 A 253 VAL VAL GLU VAL GLU LYS ARG GLY ALA GLY GLU ILE LEU SEQRES 14 A 253 LEU THR SER ILE ASP ARG ASP GLY THR LYS SER GLY ALA SEQRES 15 A 253 ASP THR GLU MET ILE ARG PHE VAL ARG PRO LEU THR THR SEQRES 16 A 253 LEU PRO ILE ILE ALA SER GLY GLY ALA GLY LYS MET GLU SEQRES 17 A 253 HIS PHE LEU GLU ALA PHE LEU ALA GLY ALA ASP ALA ALA SEQRES 18 A 253 LEU ALA ALA SER VAL PHE HIS PHE ARG GLU ILE ASP VAL SEQRES 19 A 253 ARG GLU LEU LYS GLU TYR LEU LYS LYS HIS GLY VAL ASN SEQRES 20 A 253 VAL ARG LEU GLU GLY LEU HET PO4 A 301 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *29(H2 O) HELIX 1 AA1 ASP A 31 GLY A 43 1 13 HELIX 2 AA2 ALA A 54 GLU A 71 1 18 HELIX 3 AA3 ASP A 85 ARG A 95 1 11 HELIX 4 AA4 ASN A 103 ASN A 109 1 7 HELIX 5 AA5 PRO A 110 GLY A 121 1 12 HELIX 6 AA6 LEU A 153 ARG A 163 1 11 HELIX 7 AA7 ASP A 183 ARG A 191 1 9 HELIX 8 AA8 PRO A 192 THR A 194 5 3 HELIX 9 AA9 LYS A 206 GLY A 217 1 12 HELIX 10 AB1 ALA A 224 PHE A 229 1 6 HELIX 11 AB2 ASP A 233 HIS A 244 1 12 SHEET 1 AA1 8 ARG A 16 VAL A 17 0 SHEET 2 AA1 8 ARG A 5 LYS A 13 -1 N LYS A 13 O ARG A 16 SHEET 3 AA1 8 GLU A 46 ASP A 51 1 O VAL A 48 N LEU A 10 SHEET 4 AA1 8 PHE A 77 GLY A 80 1 O THR A 78 N PHE A 49 SHEET 5 AA1 8 LYS A 99 ILE A 102 1 O LYS A 99 N VAL A 79 SHEET 6 AA1 8 VAL A 125 VAL A 134 1 O VAL A 126 N VAL A 100 SHEET 7 AA1 8 GLU A 137 THR A 142 -1 O GLU A 137 N VAL A 134 SHEET 8 AA1 8 LYS A 147 LEU A 152 -1 O THR A 149 N VAL A 140 SHEET 1 AA2 8 ARG A 16 VAL A 17 0 SHEET 2 AA2 8 ARG A 5 LYS A 13 -1 N LYS A 13 O ARG A 16 SHEET 3 AA2 8 ALA A 220 ALA A 223 1 O ALA A 221 N ILE A 7 SHEET 4 AA2 8 ILE A 198 SER A 201 1 N ALA A 200 O LEU A 222 SHEET 5 AA2 8 GLU A 167 SER A 172 1 N ILE A 168 O ILE A 199 SHEET 6 AA2 8 VAL A 125 VAL A 134 1 N ILE A 129 O LEU A 169 SHEET 7 AA2 8 GLU A 137 THR A 142 -1 O GLU A 137 N VAL A 134 SHEET 8 AA2 8 LYS A 147 LEU A 152 -1 O THR A 149 N VAL A 140 SITE 1 AC1 5 GLY A 81 GLY A 82 ASN A 103 THR A 104 SITE 2 AC1 5 HOH A 404 CRYST1 95.624 95.624 154.913 90.00 90.00 120.00 P 61 2 2 12 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 0.010458 0.006038 0.000000 0.00000 SCALE2 0.000000 0.012075 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006455 0.00000