PDB Short entry for 4C6D HEADER HYDROLASE 18-SEP-13 4C6D TITLE CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND TO TITLE 2 SUBSTRATE AT PH 6.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAD PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1456-1846; COMPND 5 SYNONYM: DIHYDROOROTASE; COMPND 6 EC: 3.4.2.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: POPIN-M KEYWDS HYDROLASE, DE NOVO PYRIMIDINE BIOSYNTHESIS, AMIDOHYDROLASE KEYWDS 2 SUPERFAMILY, METALLOENZYME, ZINC BINDING, HISTIDINATE ANION EXPDTA X-RAY DIFFRACTION AUTHOR S.RAMON-MAIQUES,N.LALLOUS,A.GRANDE-GARCIA REVDAT 3 20-DEC-23 4C6D 1 REMARK LINK ATOM REVDAT 2 19-FEB-14 4C6D 1 JRNL REVDAT 1 05-FEB-14 4C6D 0 JRNL AUTH A.GRANDE-GARCIA,N.LALLOUS,C.DIAZ-TEJADA,S.RAMON-MAIQUES JRNL TITL STRUCTURE, FUNCTIONAL CHARACTERIZATION AND EVOLUTION OF THE JRNL TITL 2 DIHYDROOROTASE DOMAIN OF HUMAN CAD. JRNL REF STRUCTURE V. 22 185 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24332717 JRNL DOI 10.1016/J.STR.2013.10.016 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 98957 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4949 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 19.8693 - 4.0226 1.00 3344 176 0.1553 0.1578 REMARK 3 2 4.0226 - 3.1971 1.00 3225 170 0.1265 0.1380 REMARK 3 3 3.1971 - 2.7943 1.00 3183 168 0.1435 0.1419 REMARK 3 4 2.7943 - 2.5393 1.00 3192 168 0.1373 0.1513 REMARK 3 5 2.5393 - 2.3576 1.00 3156 166 0.1214 0.1261 REMARK 3 6 2.3576 - 2.2188 1.00 3163 166 0.1133 0.1048 REMARK 3 7 2.2188 - 2.1078 1.00 3179 168 0.0998 0.1188 REMARK 3 8 2.1078 - 2.0162 1.00 3133 164 0.1032 0.1199 REMARK 3 9 2.0162 - 1.9386 1.00 3108 164 0.1013 0.1139 REMARK 3 10 1.9386 - 1.8718 1.00 3124 165 0.0996 0.1148 REMARK 3 11 1.8718 - 1.8133 1.00 3159 166 0.0966 0.1253 REMARK 3 12 1.8133 - 1.7615 1.00 3151 166 0.0958 0.1080 REMARK 3 13 1.7615 - 1.7152 1.00 3135 165 0.0903 0.1073 REMARK 3 14 1.7152 - 1.6733 1.00 3102 163 0.0847 0.1029 REMARK 3 15 1.6733 - 1.6353 1.00 3146 165 0.0847 0.1192 REMARK 3 16 1.6353 - 1.6005 1.00 3111 164 0.0859 0.1143 REMARK 3 17 1.6005 - 1.5685 1.00 3117 164 0.0861 0.1038 REMARK 3 18 1.5685 - 1.5389 1.00 3128 165 0.0834 0.1166 REMARK 3 19 1.5389 - 1.5115 1.00 3092 163 0.0883 0.1187 REMARK 3 20 1.5115 - 1.4858 1.00 3136 165 0.0920 0.1369 REMARK 3 21 1.4858 - 1.4619 1.00 3117 164 0.0999 0.1218 REMARK 3 22 1.4619 - 1.4394 1.00 3129 164 0.1080 0.1418 REMARK 3 23 1.4394 - 1.4182 1.00 3094 163 0.1149 0.1523 REMARK 3 24 1.4182 - 1.3983 1.00 3145 166 0.1210 0.1629 REMARK 3 25 1.3983 - 1.3794 1.00 3092 163 0.1258 0.1652 REMARK 3 26 1.3794 - 1.3615 1.00 3142 165 0.1294 0.1530 REMARK 3 27 1.3615 - 1.3444 1.00 3090 163 0.1349 0.1850 REMARK 3 28 1.3444 - 1.3283 1.00 3123 164 0.1411 0.1731 REMARK 3 29 1.3283 - 1.3128 1.00 3075 162 0.1496 0.1835 REMARK 3 30 1.3128 - 1.2981 0.93 2917 154 0.1751 0.1800 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 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 : 0.022 3097 REMARK 3 ANGLE : 1.904 4268 REMARK 3 CHIRALITY : 0.077 480 REMARK 3 PLANARITY : 0.007 558 REMARK 3 DIHEDRAL : 14.006 1159 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 4C6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1290058406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4C6C REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 30.78000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.78000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.04000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.38500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.04000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.38500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.78000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.04000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.38500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.78000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.04000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 79.38500 REMARK 290 SMTRY3 8 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: 5200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -308.6 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 C FMT A2829 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2022 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2059 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2318 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 GLY A 1454 REMARK 465 PRO A 1455 REMARK 465 MET A 1456 REMARK 465 THR A 1457 REMARK 465 SER A 1458 REMARK 465 GLN A 1459 REMARK 465 PRO A 1822 REMARK 465 SER A 1823 REMARK 465 ALA A 1824 REMARK 465 PRO A 1825 REMARK 465 ALA A 1826 REMARK 465 THR A 1827 REMARK 465 SER A 1828 REMARK 465 GLU A 1829 REMARK 465 MET A 1830 REMARK 465 THR A 1831 REMARK 465 THR A 1832 REMARK 465 THR A 1833 REMARK 465 PRO A 1834 REMARK 465 GLU A 1835 REMARK 465 ARG A 1836 REMARK 465 PRO A 1837 REMARK 465 ARG A 1838 REMARK 465 ARG A 1839 REMARK 465 GLY A 1840 REMARK 465 ILE A 1841 REMARK 465 PRO A 1842 REMARK 465 GLY A 1843 REMARK 465 LEU A 1844 REMARK 465 PRO A 1845 REMARK 465 ASP A 1846 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A1460 CG CD CE NZ REMARK 470 GLU A1651 CG CD OE1 OE2 REMARK 470 ARG A1667 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HZ3 LYS A 1482 HD1 HIS A 1690 1.28 REMARK 500 O HOH A 2040 O HOH A 2246 2.08 REMARK 500 O HOH A 2126 O HOH A 2127 2.09 REMARK 500 O HOH A 2066 O HOH A 2392 2.09 REMARK 500 O HOH A 2161 O HOH A 2185 2.11 REMARK 500 O HOH A 2049 O HOH A 2328 2.18 REMARK 500 O ASN A 1560 O HOH A 2138 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2019 O HOH A 2296 3554 2.13 REMARK 500 O HOH A 2026 O HOH A 2026 3554 2.19 REMARK 500 O HOH A 2185 O HOH A 2299 3554 2.19 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 ARG A1475 -11.62 70.12 REMARK 500 GLU A1483 155.44 177.70 REMARK 500 ASN A1505 46.39 -85.76 REMARK 500 GLU A1561 117.24 -26.64 REMARK 500 THR A1562 -169.44 -168.00 REMARK 500 THR A1562 -167.45 -161.09 REMARK 500 GLN A1593 -127.28 52.64 REMARK 500 HIS A1614 73.49 23.69 REMARK 500 HIS A1733 -68.53 -148.48 REMARK 500 ASP A1796 50.89 38.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2015 DISTANCE = 5.87 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2824 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1471 ND1 REMARK 620 2 CYS A1613 SG 111.6 REMARK 620 3 GLU A1637 OE2 84.0 114.6 REMARK 620 4 GLU A1637 OE1 124.8 115.5 51.2 REMARK 620 5 HOH A2070 O 122.2 108.1 114.9 67.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2825 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1471 NE2 REMARK 620 2 HIS A1473 NE2 116.1 REMARK 620 3 KCX A1556 OQ2 91.2 91.5 REMARK 620 4 ASP A1686 OD1 85.2 91.5 176.1 REMARK 620 5 HOH A2071 O 113.5 130.4 89.0 91.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2826 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A1556 OQ1 REMARK 620 2 HIS A1590 ND1 107.3 REMARK 620 3 HIS A1614 NE2 108.8 94.3 REMARK 620 4 HOH A2071 O 99.7 147.3 94.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2828 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1741 ND1 REMARK 620 2 HOH A2391 O 127.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DOR A 2822 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCD A 2823 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2824 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2825 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2826 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2827 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2828 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2829 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2830 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2831 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C6B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD WITH REMARK 900 INCOMPLETE ACTIVE SITE, OBTAINED RECOMBINANTLY FROM E. COLI. REMARK 900 RELATED ID: 4C6C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD IN APO- REMARK 900 FORM OBTAINED RECOMBINANTLY FROM HEK293 CELLS. REMARK 900 RELATED ID: 4C6E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND REMARK 900 TO SUBSTRATE AT PH 5.5 REMARK 900 RELATED ID: 4C6F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND REMARK 900 TO SUBSTRATE AT PH 6.5 REMARK 900 RELATED ID: 4C6I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND REMARK 900 TO SUBSTRATE AT PH 7.0 REMARK 900 RELATED ID: 4C6J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND REMARK 900 TO SUBSTRATE AT PH 7.5 REMARK 900 RELATED ID: 4C6K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND REMARK 900 TO SUBSTRATE AT PH 8.0 REMARK 900 RELATED ID: 4C6L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND REMARK 900 TO THE INHIBITOR FLUOROOROTATE AT PH 6.0 REMARK 900 RELATED ID: 4C6M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND REMARK 900 TO THE INHIBITOR FLUOROOROTATE AT PH 7.0 REMARK 900 RELATED ID: 4C6N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD E1637T REMARK 900 MUTANT BOUND TO SUBSTRATE AT PH 6.0 REMARK 900 RELATED ID: 4C6O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD C1613S REMARK 900 MUTANT IN APO-FORM AT PH 6.0 REMARK 900 RELATED ID: 4C6P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD C1613S REMARK 900 MUTANT IN APO-FORM AT PH 7.0 REMARK 900 RELATED ID: 4C6Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD C1613S REMARK 900 MUTANT BOUND TO SUBSTRATE AT PH 7.0 DBREF 4C6D A 1456 1846 UNP P27708 PYR1_HUMAN 1456 1846 SEQADV 4C6D GLY A 1454 UNP P27708 EXPRESSION TAG SEQADV 4C6D PRO A 1455 UNP P27708 EXPRESSION TAG SEQRES 1 A 393 GLY PRO MET THR SER GLN LYS LEU VAL ARG LEU PRO GLY SEQRES 2 A 393 LEU ILE ASP VAL HIS VAL HIS LEU ARG GLU PRO GLY GLY SEQRES 3 A 393 THR HIS LYS GLU ASP PHE ALA SER GLY THR ALA ALA ALA SEQRES 4 A 393 LEU ALA GLY GLY ILE THR MET VAL CYS ALA MET PRO ASN SEQRES 5 A 393 THR ARG PRO PRO ILE ILE ASP ALA PRO ALA LEU ALA LEU SEQRES 6 A 393 ALA GLN LYS LEU ALA GLU ALA GLY ALA ARG CYS ASP PHE SEQRES 7 A 393 ALA LEU PHE LEU GLY ALA SER SER GLU ASN ALA GLY THR SEQRES 8 A 393 LEU GLY THR VAL ALA GLY SER ALA ALA GLY LEU KCX LEU SEQRES 9 A 393 TYR LEU ASN GLU THR PHE SER GLU LEU ARG LEU ASP SER SEQRES 10 A 393 VAL VAL GLN TRP MET GLU HIS PHE GLU THR TRP PRO SER SEQRES 11 A 393 HIS LEU PRO ILE VAL ALA HIS ALA GLU GLN GLN THR VAL SEQRES 12 A 393 ALA ALA VAL LEU MET VAL ALA GLN LEU THR GLN ARG SER SEQRES 13 A 393 VAL HIS ILE CYS HIS VAL ALA ARG LYS GLU GLU ILE LEU SEQRES 14 A 393 LEU ILE LYS ALA ALA LYS ALA ARG GLY LEU PRO VAL THR SEQRES 15 A 393 CYS GLU VAL ALA PRO HIS HIS LEU PHE LEU SER HIS ASP SEQRES 16 A 393 ASP LEU GLU ARG LEU GLY PRO GLY LYS GLY GLU VAL ARG SEQRES 17 A 393 PRO GLU LEU GLY SER ARG GLN ASP VAL GLU ALA LEU TRP SEQRES 18 A 393 GLU ASN MET ALA VAL ILE ASP CYS PHE ALA SER ASP HIS SEQRES 19 A 393 ALA PRO HIS THR LEU GLU GLU LYS CYS GLY SER ARG PRO SEQRES 20 A 393 PRO PRO GLY PHE PRO GLY LEU GLU THR MET LEU PRO LEU SEQRES 21 A 393 LEU LEU THR ALA VAL SER GLU GLY ARG LEU SER LEU ASP SEQRES 22 A 393 ASP LEU LEU GLN ARG LEU HIS HIS ASN PRO ARG ARG ILE SEQRES 23 A 393 PHE HIS LEU PRO PRO GLN GLU ASP THR TYR VAL GLU VAL SEQRES 24 A 393 ASP LEU GLU HIS GLU TRP THR ILE PRO SER HIS MET PRO SEQRES 25 A 393 PHE SER LYS ALA HIS TRP THR PRO PHE GLU GLY GLN LYS SEQRES 26 A 393 VAL LYS GLY THR VAL ARG ARG VAL VAL LEU ARG GLY GLU SEQRES 27 A 393 VAL ALA TYR ILE ASP GLY GLN VAL LEU VAL PRO PRO GLY SEQRES 28 A 393 TYR GLY GLN ASP VAL ARG LYS TRP PRO GLN GLY ALA VAL SEQRES 29 A 393 PRO GLN LEU PRO PRO SER ALA PRO ALA THR SER GLU MET SEQRES 30 A 393 THR THR THR PRO GLU ARG PRO ARG ARG GLY ILE PRO GLY SEQRES 31 A 393 LEU PRO ASP MODRES 4C6D KCX A 1556 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A1556 22 HET DOR A2822 16 HET NCD A2823 18 HET ZN A2824 1 HET ZN A2825 1 HET ZN A2826 1 HET FMT A2827 4 HET ZN A2828 1 HET FMT A2829 4 HET FMT A2830 4 HET FMT A2831 4 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM DOR (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID HETNAM NCD N-CARBAMOYL-L-ASPARTATE HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID HETSYN DOR DIHYDROOROTIC ACID FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 DOR C5 H6 N2 O4 FORMUL 3 NCD C5 H8 N2 O5 FORMUL 4 ZN 4(ZN 2+) FORMUL 7 FMT 4(C H2 O2) FORMUL 12 HOH *392(H2 O) HELIX 1 1 ASP A 1484 GLY A 1495 1 12 HELIX 2 2 ASP A 1512 ALA A 1527 1 16 HELIX 3 3 VAL A 1548 ALA A 1552 5 5 HELIX 4 4 SER A 1570 TRP A 1581 1 12 HELIX 5 5 GLN A 1593 THR A 1606 1 14 HELIX 6 6 ARG A 1617 ARG A 1630 1 14 HELIX 7 7 ALA A 1639 LEU A 1645 1 7 HELIX 8 8 SER A 1646 ASP A 1648 5 3 HELIX 9 9 ASP A 1649 GLY A 1658 1 10 HELIX 10 10 SER A 1666 ASN A 1676 1 11 HELIX 11 11 MET A 1677 ILE A 1680 5 4 HELIX 12 12 THR A 1691 CYS A 1696 1 6 HELIX 13 13 GLY A 1706 GLU A 1720 1 15 HELIX 14 14 SER A 1724 HIS A 1733 1 10 HELIX 15 15 HIS A 1733 HIS A 1741 1 9 HELIX 16 16 VAL A 1809 ALA A 1816 5 8 SHEET 1 AA 5 VAL A1462 PRO A1465 0 SHEET 2 AA 5 TYR A1749 THR A1759 -1 O VAL A1750 N LEU A1464 SHEET 3 AA 5 LYS A1778 LEU A1788 -1 O VAL A1779 N TRP A1758 SHEET 4 AA 5 GLU A1791 ILE A1795 -1 O GLU A1791 N LEU A1788 SHEET 5 AA 5 GLN A1798 VAL A1799 -1 O GLN A1798 N ILE A1795 SHEET 1 AB 3 LEU A1467 VAL A1472 0 SHEET 2 AB 3 ILE A1497 ALA A1502 1 N THR A1498 O LEU A1467 SHEET 3 AB 3 ASP A1530 LEU A1533 1 O ASP A1530 N VAL A1500 SHEET 1 AC 6 LEU A1535 GLY A1536 0 SHEET 2 AC 6 LEU A1555 TYR A1558 1 N KCX A1556 O LEU A1535 SHEET 3 AC 6 ILE A1587 HIS A1590 1 O VAL A1588 N LEU A1557 SHEET 4 AC 6 VAL A1610 ILE A1612 1 O HIS A1611 N ALA A1589 SHEET 5 AC 6 VAL A1634 VAL A1638 1 O THR A1635 N ILE A1612 SHEET 6 AC 6 CYS A1682 PHE A1683 1 O CYS A1682 N VAL A1638 SSBOND 1 CYS A 1696 CYS A 1696 1555 3454 2.05 LINK C LEU A1555 N KCX A1556 1555 1555 1.33 LINK C KCX A1556 N LEU A1557 1555 1555 1.35 LINK ND1 HIS A1471 ZN ZN A2824 1555 1555 2.07 LINK NE2 HIS A1471 ZN ZN A2825 1555 1555 2.01 LINK NE2 HIS A1473 ZN ZN A2825 1555 1555 2.04 LINK OQ2 KCX A1556 ZN ZN A2825 1555 1555 2.23 LINK OQ1 KCX A1556 ZN ZN A2826 1555 1555 1.89 LINK ND1 HIS A1590 ZN ZN A2826 1555 1555 2.05 LINK SG CYS A1613 ZN ZN A2824 1555 1555 2.41 LINK NE2 HIS A1614 ZN ZN A2826 1555 1555 2.04 LINK OE2 GLU A1637 ZN ZN A2824 1555 1555 2.12 LINK OE1 GLU A1637 ZN ZN A2824 1555 1555 2.69 LINK OD1 ASP A1686 ZN ZN A2825 1555 1555 2.15 LINK ND1 HIS A1741 ZN ZN A2828 1555 1555 2.24 LINK O HOH A2070 ZN ZN A2824 1555 1555 2.06 LINK O HOH A2071 ZN ZN A2825 1555 1555 2.08 LINK O HOH A2071 ZN ZN A2826 1555 1555 2.08 LINK O HOH A2391 ZN ZN A2828 1555 1555 2.23 CISPEP 1 GLU A 1476 PRO A 1477 0 5.09 CISPEP 2 ARG A 1507 PRO A 1508 0 2.26 CISPEP 3 ARG A 1661 PRO A 1662 0 -8.42 SITE 1 AC1 15 HIS A1473 ARG A1475 ASN A1505 THR A1562 SITE 2 AC1 15 PHE A1563 HIS A1590 VAL A1660 ARG A1661 SITE 3 AC1 15 ALA A1688 HIS A1690 PRO A1702 GLY A1703 SITE 4 AC1 15 HOH A2071 ZN A2825 ZN A2826 SITE 1 AC2 19 HIS A1471 HIS A1473 ARG A1475 ASN A1505 SITE 2 AC2 19 KCX A1556 THR A1562 PHE A1563 HIS A1590 SITE 3 AC2 19 HIS A1614 VAL A1660 ARG A1661 ASP A1686 SITE 4 AC2 19 ALA A1688 HIS A1690 PRO A1702 GLY A1703 SITE 5 AC2 19 HOH A2071 ZN A2825 ZN A2826 SITE 1 AC3 5 HIS A1471 MET A1503 CYS A1613 GLU A1637 SITE 2 AC3 5 HOH A2070 SITE 1 AC4 8 HIS A1471 HIS A1473 KCX A1556 ASP A1686 SITE 2 AC4 8 HOH A2071 DOR A2822 NCD A2823 ZN A2826 SITE 1 AC5 7 KCX A1556 HIS A1590 HIS A1614 HOH A2071 SITE 2 AC5 7 DOR A2822 NCD A2823 ZN A2825 SITE 1 AC6 8 PRO A1586 ILE A1587 ARG A1608 SER A1609 SITE 2 AC6 8 VAL A1610 HIS A1611 HOH A2183 HOH A2215 SITE 1 AC7 4 HIS A1734 HIS A1741 HOH A2298 HOH A2391 SITE 1 AC8 2 HIS A1734 ARG A1737 SITE 1 AC9 7 ARG A1463 THR A1748 TYR A1749 GLN A1814 SITE 2 AC9 7 HOH A2066 HOH A2320 HOH A2392 SITE 1 BC1 4 GLN A1604 LEU A1605 ARG A1630 HOH A2209 CRYST1 82.080 158.770 61.560 90.00 90.00 90.00 C 2 2 21 8 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 0.012183 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016244 0.00000