HEADER HYDROLASE 18-SEP-13 4C6I
TITLE CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND TO
TITLE 2 SUBSTRATE AT PH 7.0
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CAD PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 1456-1822;
COMPND 5 SYNONYM: DIHYDROOROTASE;
COMPND 6 EC: 3.5.2.3;
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 4C6I 1 REMARK LINK ATOM
REVDAT 2 19-FEB-14 4C6I 1 JRNL
REVDAT 1 08-JAN-14 4C6I 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. 1.35 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) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.00
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1
REMARK 3 NUMBER OF REFLECTIONS : 87043
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.124
REMARK 3 R VALUE (WORKING SET) : 0.123
REMARK 3 FREE R VALUE : 0.145
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 8340
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 47.0367 - 4.1847 0.98 5329 283 0.1456 0.1558
REMARK 3 2 4.1847 - 3.3218 0.99 5378 283 0.1181 0.1499
REMARK 3 3 3.3218 - 2.9020 1.00 5410 284 0.1301 0.1479
REMARK 3 4 2.9020 - 2.6367 0.99 5361 283 0.1284 0.1214
REMARK 3 5 2.6367 - 2.4477 0.97 5267 276 0.1168 0.1349
REMARK 3 6 2.4477 - 2.3034 0.99 5362 279 0.1053 0.1357
REMARK 3 7 2.3034 - 2.1880 0.99 5391 284 0.1020 0.1145
REMARK 3 8 2.1880 - 2.0928 0.99 5369 277 0.0967 0.1190
REMARK 3 9 2.0928 - 2.0122 0.99 5378 279 0.1030 0.1317
REMARK 3 10 2.0122 - 1.9428 0.99 5432 286 0.0985 0.1083
REMARK 3 11 1.9428 - 1.8820 0.99 5383 289 0.1040 0.1370
REMARK 3 12 1.8820 - 1.8282 0.99 5315 283 0.1054 0.1189
REMARK 3 13 1.8282 - 1.7801 0.98 5356 283 0.1068 0.1392
REMARK 3 14 1.7801 - 1.7367 0.99 5408 284 0.1086 0.1347
REMARK 3 15 1.7367 - 1.6972 0.99 5388 283 0.1030 0.1258
REMARK 3 16 1.6972 - 1.6611 0.99 5357 287 0.1031 0.1413
REMARK 3 17 1.6611 - 1.6278 0.99 5332 282 0.1052 0.1222
REMARK 3 18 1.6278 - 1.5971 0.98 5381 284 0.1075 0.1407
REMARK 3 19 1.5971 - 1.5686 0.97 5247 271 0.1142 0.1443
REMARK 3 20 1.5686 - 1.5420 0.97 5328 277 0.1210 0.1666
REMARK 3 21 1.5420 - 1.5171 0.97 5318 282 0.1315 0.1881
REMARK 3 22 1.5171 - 1.4938 0.97 5235 274 0.1352 0.1546
REMARK 3 23 1.4938 - 1.4718 0.96 5261 285 0.1463 0.2011
REMARK 3 24 1.4718 - 1.4511 0.96 5244 275 0.1634 0.1900
REMARK 3 25 1.4511 - 1.4315 0.95 5081 270 0.1651 0.2010
REMARK 3 26 1.4315 - 1.4129 0.95 5195 277 0.1750 0.2188
REMARK 3 27 1.4129 - 1.3952 0.94 4996 263 0.1794 0.2157
REMARK 3 28 1.3952 - 1.3784 0.94 5180 275 0.1921 0.2128
REMARK 3 29 1.3784 - 1.3624 0.93 5118 268 0.2155 0.2442
REMARK 3 30 1.3624 - 1.3471 0.83 4488 234 0.2357 0.2715
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) : 0.090
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.780
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) : 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 : 0.018 3144
REMARK 3 ANGLE : 1.311 4340
REMARK 3 CHIRALITY : 0.079 487
REMARK 3 PLANARITY : 0.007 571
REMARK 3 DIHEDRAL : 14.332 1195
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 4C6I 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_1290058416.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-MAY-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
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 : 87043
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 47.010
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2
REMARK 200 DATA REDUNDANCY : 6.400
REMARK 200 R MERGE (I) : 0.05000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0
REMARK 200 DATA REDUNDANCY IN SHELL : 6.30
REMARK 200 R MERGE FOR SHELL (I) : 0.61000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400
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 7.0
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 30.75150
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 30.75150
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 41.03600
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.34350
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.03600
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.34350
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.75150
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.03600
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.34350
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.75150
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.03600
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 79.34350
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: 4900 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25840 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -261.4 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 A2828 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2031 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2075 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2077 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2351 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 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 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 HD1 HIS A 1611 HG1 THR A 1635 1.32
REMARK 500 HZ3 LYS A 1482 HD1 HIS A 1690 1.32
REMARK 500 O HOH A 2182 O HOH A 2207 1.97
REMARK 500 OG SER A 1719 O HOH A 2306 2.18
REMARK 500 O HOH A 2331 O HOH A 2332 2.19
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 2207 O HOH A 2329 3554 2.10
REMARK 500 O HOH A 2328 O HOH A 2344 3554 2.14
REMARK 500 O HOH A 2035 O HOH A 2035 3554 2.15
REMARK 500 O HOH A 2182 O HOH A 2330 3554 2.16
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 HIS A1471 89.88 -151.09
REMARK 500 ARG A1475 -7.65 69.31
REMARK 500 GLU A1483 154.56 177.78
REMARK 500 ASN A1505 46.71 -86.29
REMARK 500 ASN A1560 -146.23 -120.21
REMARK 500 THR A1562 -169.52 -169.79
REMARK 500 GLN A1593 -125.61 51.87
REMARK 500 HIS A1614 73.78 22.36
REMARK 500 HIS A1733 -67.64 -147.95
REMARK 500 ASP A1796 51.04 39.76
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 A2021 DISTANCE = 5.86 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 A2823 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A1471 NE2
REMARK 620 2 HIS A1473 NE2 116.6
REMARK 620 3 KCX A1556 OQ2 90.1 91.3
REMARK 620 4 ASP A1686 OD1 85.8 92.4 175.5
REMARK 620 5 HOH A2088 O 112.2 131.2 88.2 91.5
REMARK 620 6 NCD A2831 O5 128.4 114.8 84.4 96.6 16.8
REMARK 620 N 1 2 3 4 5
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 ND1
REMARK 620 2 CYS A1613 SG 113.3
REMARK 620 3 GLU A1637 OE2 90.0 114.2
REMARK 620 4 HOH A2087 O 119.4 111.1 107.1
REMARK 620 N 1 2 3
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 KCX A1556 OQ1
REMARK 620 2 HIS A1590 ND1 107.2
REMARK 620 3 HIS A1614 NE2 109.3 93.6
REMARK 620 4 HOH A2088 O 98.3 149.0 94.3
REMARK 620 5 NCD A2831 O4 116.4 85.9 132.2 66.8
REMARK 620 6 NCD A2831 O5 95.6 142.1 107.2 13.0 56.6
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2823
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2824
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2825
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2827
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2828
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2829
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DOR A 2830
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCD 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: 4C6D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD BOUND
REMARK 900 TO SUBSTRATE AT PH 6.0
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: 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 4C6I A 1456 1846 UNP P27708 PYR1_HUMAN 1456 1846
SEQADV 4C6I GLY A 1454 UNP P27708 EXPRESSION TAG
SEQADV 4C6I 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 4C6I KCX A 1556 LYS LYSINE NZ-CARBOXYLIC ACID
HET KCX A1556 23
HET ZN A2823 1
HET ZN A2824 1
HET ZN A2825 1
HET FMT A2827 4
HET FMT A2828 4
HET FMT A2829 4
HET DOR A2830 16
HET NCD A2831 18
HETNAM KCX LYSINE NZ-CARBOXYLIC ACID
HETNAM ZN ZINC ION
HETNAM FMT FORMIC ACID
HETNAM DOR (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
HETNAM NCD N-CARBAMOYL-L-ASPARTATE
HETSYN DOR DIHYDROOROTIC ACID
FORMUL 1 KCX C7 H14 N2 O4
FORMUL 2 ZN 3(ZN 2+)
FORMUL 5 FMT 3(C H2 O2)
FORMUL 8 DOR C5 H6 N2 O4
FORMUL 9 NCD C5 H8 N2 O5
FORMUL 10 HOH *424(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 GLY A 1697 1 7
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 2.49
LINK C LEU A1555 N KCX A1556 1555 1555 1.34
LINK C KCX A1556 N LEU A1557 1555 1555 1.34
LINK NE2 HIS A1471 ZN ZN A2823 1555 1555 2.01
LINK ND1 HIS A1471 ZN ZN A2825 1555 1555 2.02
LINK NE2 HIS A1473 ZN ZN A2823 1555 1555 2.03
LINK OQ2 KCX A1556 ZN ZN A2823 1555 1555 2.26
LINK OQ1 KCX A1556 ZN ZN A2824 1555 1555 1.89
LINK ND1 HIS A1590 ZN ZN A2824 1555 1555 2.07
LINK SG CYS A1613 ZN ZN A2825 1555 1555 2.33
LINK NE2 HIS A1614 ZN ZN A2824 1555 1555 2.05
LINK OE2 GLU A1637 ZN ZN A2825 1555 1555 2.08
LINK OD1 ASP A1686 ZN ZN A2823 1555 1555 2.12
LINK O HOH A2087 ZN ZN A2825 1555 1555 2.03
LINK O HOH A2088 ZN ZN A2823 1555 1555 2.05
LINK O HOH A2088 ZN ZN A2824 1555 1555 2.10
LINK ZN ZN A2823 O5 BNCD A2831 1555 1555 1.95
LINK ZN ZN A2824 O4 BNCD A2831 1555 1555 2.06
LINK ZN ZN A2824 O5 BNCD A2831 1555 1555 2.40
CISPEP 1 GLU A 1476 PRO A 1477 0 5.72
CISPEP 2 ARG A 1507 PRO A 1508 0 1.39
CISPEP 3 ARG A 1661 PRO A 1662 0 -10.20
SITE 1 AC1 7 HIS A1471 HIS A1473 KCX A1556 ASP A1686
SITE 2 AC1 7 HOH A2088 ZN A2824 DOR A2830
SITE 1 AC2 6 KCX A1556 HIS A1590 HIS A1614 HOH A2088
SITE 2 AC2 6 ZN A2823 DOR A2830
SITE 1 AC3 5 HIS A1471 MET A1503 CYS A1613 GLU A1637
SITE 2 AC3 5 HOH A2087
SITE 1 AC4 8 PRO A1586 ILE A1587 ARG A1608 SER A1609
SITE 2 AC4 8 VAL A1610 HIS A1611 HOH A2205 HOH A2236
SITE 1 AC5 2 HIS A1734 ARG A1737
SITE 1 AC6 4 GLN A1604 LEU A1605 ARG A1630 HOH A2230
SITE 1 AC7 15 HIS A1473 ARG A1475 ASN A1505 THR A1562
SITE 2 AC7 15 PHE A1563 HIS A1590 VAL A1660 ARG A1661
SITE 3 AC7 15 ALA A1688 HIS A1690 PRO A1702 GLY A1703
SITE 4 AC7 15 HOH A2088 ZN A2823 ZN A2824
SITE 1 AC8 19 HIS A1471 HIS A1473 ARG A1475 ASN A1505
SITE 2 AC8 19 KCX A1556 THR A1562 PHE A1563 HIS A1590
SITE 3 AC8 19 HIS A1614 VAL A1660 ARG A1661 ASP A1686
SITE 4 AC8 19 ALA A1688 HIS A1690 PRO A1702 GLY A1703
SITE 5 AC8 19 HOH A2088 ZN A2823 ZN A2824
CRYST1 82.072 158.687 61.503 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 0.012184 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006302 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016259 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
