HEADER LYASE 14-JAN-12 4DBD TITLE CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM TITLE 2 SULFOLOBUS SOLFATARICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OMP DECARBOXYLASE; COMPND 5 EC: 4.1.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 555311; SOURCE 4 STRAIN: 98/2; SOURCE 5 GENE: PYRF, SSOL_1680; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TIM BARREL, OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE, OROTIDINE 5'- KEYWDS 2 MONOPHOSPHATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,B.DESAI,J.A.GERLT,S.C.ALMO REVDAT 2 13-SEP-23 4DBD 1 REMARK REVDAT 1 13-FEB-13 4DBD 0 JRNL AUTH A.A.FEDOROV,E.V.FEDOROV,B.DESAI,J.A.GERLT,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE JRNL TITL 2 DECARBOXYLASE FROM SULFOLOBUS SOLFATARICUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 21586 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) : 0.208 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1107 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 36.6270 - 3.3979 1.00 2757 138 0.1832 0.2007 REMARK 3 2 3.3979 - 2.6973 1.00 2614 135 0.2122 0.2116 REMARK 3 3 2.6973 - 2.3564 1.00 2587 154 0.2129 0.3078 REMARK 3 4 2.3564 - 2.1410 1.00 2561 141 0.2114 0.2784 REMARK 3 5 2.1410 - 1.9875 1.00 2573 132 0.2141 0.2459 REMARK 3 6 1.9875 - 1.8703 1.00 2539 157 0.2147 0.2773 REMARK 3 7 1.8703 - 1.7767 1.00 2528 128 0.2612 0.3045 REMARK 3 8 1.7767 - 1.6993 0.91 2320 122 0.3067 0.3604 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.40 REMARK 3 SHRINKAGE RADIUS : 1.17 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 29.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.72290 REMARK 3 B22 (A**2) : 10.76790 REMARK 3 B33 (A**2) : -6.04500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 1705 REMARK 3 ANGLE : 0.992 2303 REMARK 3 CHIRALITY : 0.071 262 REMARK 3 PLANARITY : 0.004 289 REMARK 3 DIHEDRAL : 13.397 638 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 4DBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21586 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.699 REMARK 200 RESOLUTION RANGE LOW (A) : 36.618 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL 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: 3VE9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M LITHIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE, 0.5M AMMONIUM SULFATE, PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 20.18350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.40950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.18350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.40950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -129.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 303 LIES ON A SPECIAL POSITION. 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 213 REMARK 465 CYS A 214 REMARK 465 LYS A 215 REMARK 465 GLY A 216 REMARK 465 ALA A 217 REMARK 465 ILE A 218 REMARK 465 PHE A 219 REMARK 465 ARG A 220 REMARK 465 LYS A 221 REMARK 465 LYS A 222 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 ALA A 63 62.42 -156.98 REMARK 500 VAL A 90 -66.40 -97.73 REMARK 500 SER A 93 -91.54 -138.56 REMARK 500 LYS A 145 65.85 -108.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VE7 RELATED DB: PDB REMARK 900 RELATED ID: 3VE9 RELATED DB: PDB REMARK 900 RELATED ID: 4DBE RELATED DB: PDB DBREF 4DBD A 1 222 UNP D0KT28 D0KT28_SULS9 1 222 SEQRES 1 A 222 MET LEU LYS SER ARG VAL ILE LEU ALA MET ASP LYS PRO SEQRES 2 A 222 LEU SER TYR GLN VAL LEU LYS GLU MET GLU ASN GLU LEU SEQRES 3 A 222 TYR GLY ILE LYS VAL GLY LEU PRO LEU VAL LEU ASP LEU SEQRES 4 A 222 GLY VAL ASP LYS THR ARG GLU LEU LEU ILE GLY LEU ASP SEQRES 5 A 222 VAL GLU GLU ILE ILE VAL ASP PHE LYS LEU ALA ASP ILE SEQRES 6 A 222 GLY TYR ILE MET LYS SER ILE VAL GLU ARG LEU SER PHE SEQRES 7 A 222 ALA ASN SER PHE ILE ALA HIS SER PHE ILE GLY VAL LYS SEQRES 8 A 222 GLY SER LEU ASP GLU LEU LYS ARG TYR LEU ASP ALA ASN SEQRES 9 A 222 SER LYS ASN LEU TYR LEU VAL ALA VAL MET SER HIS GLU SEQRES 10 A 222 GLY TRP SER THR LEU PHE ALA ASP TYR ILE LYS ASN VAL SEQRES 11 A 222 ILE ARG GLU ILE SER PRO LYS GLY ILE VAL VAL GLY GLY SEQRES 12 A 222 THR LYS LEU ASP HIS ILE THR GLN TYR ARG ARG ASP PHE SEQRES 13 A 222 GLU LYS MET THR ILE VAL SER PRO GLY MET GLY SER GLN SEQRES 14 A 222 GLY GLY SER TYR GLY ASP ALA VAL CYS ALA GLY ALA ASP SEQRES 15 A 222 TYR GLU ILE ILE GLY ARG SER ILE TYR ASN ALA GLY ASN SEQRES 16 A 222 PRO LEU THR ALA LEU ARG THR ILE ASN LYS ILE ILE GLU SEQRES 17 A 222 ASP LYS VAL MET LYS CYS LYS GLY ALA ILE PHE ARG LYS SEQRES 18 A 222 LYS HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *82(H2 O) HELIX 1 1 SER A 15 GLU A 23 1 9 HELIX 2 2 ASN A 24 LEU A 26 5 3 HELIX 3 3 LEU A 33 GLY A 40 1 8 HELIX 4 4 GLY A 40 ILE A 49 1 10 HELIX 5 5 ILE A 65 GLU A 74 1 10 HELIX 6 6 SER A 93 ASN A 104 1 12 HELIX 7 7 PHE A 123 SER A 135 1 13 HELIX 8 8 LYS A 145 PHE A 156 1 12 HELIX 9 9 GLY A 174 GLY A 180 1 7 HELIX 10 10 GLY A 187 ASN A 192 1 6 HELIX 11 11 ASN A 195 VAL A 211 1 17 SHEET 1 A 9 VAL A 6 MET A 10 0 SHEET 2 A 9 GLY A 28 GLY A 32 1 O LYS A 30 N LEU A 8 SHEET 3 A 9 GLU A 55 LEU A 62 1 O ILE A 57 N VAL A 31 SHEET 4 A 9 SER A 81 HIS A 85 1 O HIS A 85 N LEU A 62 SHEET 5 A 9 ASN A 107 VAL A 113 1 O TYR A 109 N PHE A 82 SHEET 6 A 9 GLY A 138 VAL A 141 1 O VAL A 140 N ALA A 112 SHEET 7 A 9 THR A 160 SER A 163 1 O VAL A 162 N VAL A 141 SHEET 8 A 9 TYR A 183 ILE A 186 1 O ILE A 185 N SER A 163 SHEET 9 A 9 VAL A 6 MET A 10 1 N ILE A 7 O GLU A 184 SITE 1 AC1 7 GLN A 169 GLY A 187 ARG A 188 HOH A 407 SITE 2 AC1 7 HOH A 419 HOH A 431 HOH A 451 SITE 1 AC2 2 THR A 121 HIS A 148 SITE 1 AC3 3 GLY A 40 VAL A 41 HOH A 438 CRYST1 40.367 64.819 73.237 90.00 90.00 90.00 P 21 21 2 4 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 0.024773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015428 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013654 0.00000