10 20 30 40 50 60 70 80 2Z26 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 17-MAY-07 2Z26
TITLE THR110ALA DIHYDROOROTASE FROM E. COLI
CAVEAT 2Z26 CHIRALITY ERROR AT THE CA CENTER OF GLN B 319.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHOASE; COMPND 5 EC: 3.5.2.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PYRC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: X7014A; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBLUESCRIPT
KEYWDS TIM BARREL, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.LEE,M.J.MAHER,J.M.GUSS
REVDAT 2 24-FEB-09 2Z26 1 VERSN REVDAT 1 09-OCT-07 2Z26 0
JRNL AUTH M.LEE,M.J.MAHER,R.I.CHRISTOPHERSON,J.M.GUSS JRNL TITL KINETIC AND STRUCTURAL ANALYSIS OF MUTANT JRNL TITL 2 ESCHERICHIA COLI DIHYDROOROTASES: A FLEXIBLE LOOP JRNL TITL 3 STABILIZES THE TRANSITION STATE JRNL REF BIOCHEMISTRY V. 46 10538 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17711307 JRNL DOI 10.1021/BI701098E
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 166743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8407 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6383 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.1560 REMARK 3 BIN FREE R VALUE SET COUNT : 335 REMARK 3 BIN FREE R VALUE : 0.2000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5464 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 782 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : 0.02000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.102 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5542 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5105 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7571 ; 1.354 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11792 ; 0.831 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 712 ; 6.198 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 240 ;31.197 ;23.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 873 ;10.455 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;14.488 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 878 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6237 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1140 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1063 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5315 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2721 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3211 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 468 ; 0.110 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.059 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.207 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.243 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.188 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3693 ; 3.590 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1393 ; 3.490 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5651 ; 4.087 ; 6.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2194 ; 4.168 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1907 ; 5.347 ; 6.000 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 11661 ; 2.440 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 786 ;12.383 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 10513 ; 6.448 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2Z26 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-07. REMARK 100 THE RCSB ID CODE IS RCSB027426.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYOCOOLED REMARK 200 SI(III) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 166743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFINEMENT REMARK 200 STARTING MODEL: 1XGE REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG3350, 0.1M MES, 75MM MGCL2, REMARK 280 0.15M KCL, PH 6.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.74650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.04550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.44250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 90.04550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.74650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.44250 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 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 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 THR A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 347 REMARK 465 THR B 1 REMARK 465 ALA B 2 REMARK 465 PRO B 3 REMARK 465 ASN B 107 REMARK 465 ALA B 108 REMARK 465 THR B 109 REMARK 465 ALA B 110 REMARK 465 ASN B 111 REMARK 465 SER B 112 REMARK 465 SER B 113 REMARK 465 HIS B 114 REMARK 465 GLN B 347
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 GLU A 317 CG CD OE1 OE2
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 53 CG CD OE1 OE2 REMARK 480 ARG A 155 NE CZ NH1 NH2 REMARK 480 GLU A 158 CG CD OE1 OE2 REMARK 480 GLU A 192 CD OE1 OE2 REMARK 480 GLN A 301 CG CD OE1 NE2 REMARK 480 ARG A 316 NE CZ NH1 NH2 REMARK 480 GLN A 319 CG CD OE1 NE2 REMARK 480 GLN A 320 CG CD OE1 NE2 REMARK 480 LYS A 346 CG CD CE NZ REMARK 480 GLU B 34 CD OE1 OE2 REMARK 480 GLU B 53 CG CD OE1 OE2 REMARK 480 LYS B 131 CG CD CE NZ REMARK 480 HIS B 144 CG ND1 CD2 CE1 NE2 REMARK 480 ASP B 146 CG OD1 OD2 REMARK 480 GLU B 158 CG CD OE1 OE2 REMARK 480 ARG B 167 CD NE CZ NH1 NH2 REMARK 480 GLU B 192 CG CD OE1 OE2 REMARK 480 ARG B 193 NE CZ NH1 NH2 REMARK 480 GLN B 301 CD OE1 NE2 REMARK 480 GLU B 317 CG CD OE1 OE2 REMARK 480 GLU B 318 CG CD OE1 OE2 REMARK 480 GLN B 319 CB CG CD OE1 NE2 REMARK 480 GLN B 320 CB CG CD OE1 NE2 REMARK 480 GLU B 339 OE1 OE2
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 A 16 103.45 -161.45 REMARK 500 ARG A 20 -152.02 59.52 REMARK 500 VAL A 160 -55.28 -126.67 REMARK 500 HIS A 177 66.64 31.15 REMARK 500 GLU A 260 69.60 -101.24 REMARK 500 ASP A 330 -160.22 64.45 REMARK 500 HIS B 16 102.77 -163.20 REMARK 500 ARG B 20 -150.18 58.02 REMARK 500 VAL B 160 -53.38 -126.45 REMARK 500 HIS B 177 65.14 31.45 REMARK 500 VAL B 297 -45.29 -132.02 REMARK 500 ASP B 330 -173.67 72.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLN B 319 -34.3 L D WRONG HAND 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 A1753 DISTANCE = 5.59 ANGSTROMS REMARK 525 HOH B1760 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A1807 DISTANCE = 5.50 ANGSTROMS
REMARK 600 REMARK 600 HETEROGEN REMARK 600 NCD(1420) AND DOR(1430) ARE IN ALTERNATE CONFORMATIONS REMARK 600 OF EACH OTHER.
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 A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 16 NE2 REMARK 620 2 HIS A 18 NE2 116.7 REMARK 620 3 KCX A 102 OQ1 89.5 92.2 REMARK 620 4 ASP A 250 OD1 85.7 89.4 175.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 102 OQ2 REMARK 620 2 HIS A 139 ND1 104.6 REMARK 620 3 HIS A 177 NE2 104.6 96.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 16 NE2 REMARK 620 2 HIS B 18 NE2 116.2 REMARK 620 3 KCX B 102 OQ1 90.0 92.1 REMARK 620 4 ASP B 250 OD1 85.2 89.6 175.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX B 102 OQ2 REMARK 620 2 HIS B 139 ND1 108.1 REMARK 620 3 HIS B 177 NE2 104.5 97.0 REMARK 620 N 1 2
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 400 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 400 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DOR A 1410 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCD B 1420 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DOR B 1430 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 1440
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XGE RELATED DB: PDB REMARK 900 WILD-TYPE DIHDYROOROTASE FROM E. COLI REMARK 900 RELATED ID: 2Z24 RELATED DB: PDB REMARK 900 RELATED ID: 2Z25 RELATED DB: PDB REMARK 900 RELATED ID: 2Z27 RELATED DB: PDB REMARK 900 RELATED ID: 2Z28 RELATED DB: PDB REMARK 900 RELATED ID: 2Z29 RELATED DB: PDB REMARK 900 RELATED ID: 2Z2A RELATED DB: PDB REMARK 900 RELATED ID: 2Z2B RELATED DB: PDB
DBREF 2Z26 A 1 347 UNP P05020 PYRC_ECOLI 2 348 DBREF 2Z26 B 1 347 UNP P05020 PYRC_ECOLI 2 348
SEQADV 2Z26 ALA A 110 UNP P05020 THR 111 ENGINEERED SEQADV 2Z26 VAL A 119 UNP P05020 ILE 120 CONFLICT SEQADV 2Z26 ALA B 110 UNP P05020 THR 111 ENGINEERED SEQADV 2Z26 VAL B 119 UNP P05020 ILE 120 CONFLICT
SEQRES 1 A 347 THR ALA PRO SER GLN VAL LEU LYS ILE ARG ARG PRO ASP SEQRES 2 A 347 ASP TRP HIS LEU HIS LEU ARG ASP GLY ASP MET LEU LYS SEQRES 3 A 347 THR VAL VAL PRO TYR THR SER GLU ILE TYR GLY ARG ALA SEQRES 4 A 347 ILE VAL MET PRO ASN LEU ALA PRO PRO VAL THR THR VAL SEQRES 5 A 347 GLU ALA ALA VAL ALA TYR ARG GLN ARG ILE LEU ASP ALA SEQRES 6 A 347 VAL PRO ALA GLY HIS ASP PHE THR PRO LEU MET THR CYS SEQRES 7 A 347 TYR LEU THR ASP SER LEU ASP PRO ASN GLU LEU GLU ARG SEQRES 8 A 347 GLY PHE ASN GLU GLY VAL PHE THR ALA ALA KCX LEU TYR SEQRES 9 A 347 PRO ALA ASN ALA THR ALA ASN SER SER HIS GLY VAL THR SEQRES 10 A 347 SER VAL ASP ALA ILE MET PRO VAL LEU GLU ARG MET GLU SEQRES 11 A 347 LYS ILE GLY MET PRO LEU LEU VAL HIS GLY GLU VAL THR SEQRES 12 A 347 HIS ALA ASP ILE ASP ILE PHE ASP ARG GLU ALA ARG PHE SEQRES 13 A 347 ILE GLU SER VAL MET GLU PRO LEU ARG GLN ARG LEU THR SEQRES 14 A 347 ALA LEU LYS VAL VAL PHE GLU HIS ILE THR THR LYS ASP SEQRES 15 A 347 ALA ALA ASP TYR VAL ARG ASP GLY ASN GLU ARG LEU ALA SEQRES 16 A 347 ALA THR ILE THR PRO GLN HIS LEU MET PHE ASN ARG ASN SEQRES 17 A 347 HIS MET LEU VAL GLY GLY VAL ARG PRO HIS LEU TYR CYS SEQRES 18 A 347 LEU PRO ILE LEU LYS ARG ASN ILE HIS GLN GLN ALA LEU SEQRES 19 A 347 ARG GLU LEU VAL ALA SER GLY PHE ASN ARG VAL PHE LEU SEQRES 20 A 347 GLY THR ASP SER ALA PRO HIS ALA ARG HIS ARG LYS GLU SEQRES 21 A 347 SER SER CYS GLY CYS ALA GLY CYS PHE ASN ALA PRO THR SEQRES 22 A 347 ALA LEU GLY SER TYR ALA THR VAL PHE GLU GLU MET ASN SEQRES 23 A 347 ALA LEU GLN HIS PHE GLU ALA PHE CYS SER VAL ASN GLY SEQRES 24 A 347 PRO GLN PHE TYR GLY LEU PRO VAL ASN ASP THR PHE ILE SEQRES 25 A 347 GLU LEU VAL ARG GLU GLU GLN GLN VAL ALA GLU SER ILE SEQRES 26 A 347 ALA LEU THR ASP ASP THR LEU VAL PRO PHE LEU ALA GLY SEQRES 27 A 347 GLU THR VAL ARG TRP SER VAL LYS GLN SEQRES 1 B 347 THR ALA PRO SER GLN VAL LEU LYS ILE ARG ARG PRO ASP SEQRES 2 B 347 ASP TRP HIS LEU HIS LEU ARG ASP GLY ASP MET LEU LYS SEQRES 3 B 347 THR VAL VAL PRO TYR THR SER GLU ILE TYR GLY ARG ALA SEQRES 4 B 347 ILE VAL MET PRO ASN LEU ALA PRO PRO VAL THR THR VAL SEQRES 5 B 347 GLU ALA ALA VAL ALA TYR ARG GLN ARG ILE LEU ASP ALA SEQRES 6 B 347 VAL PRO ALA GLY HIS ASP PHE THR PRO LEU MET THR CYS SEQRES 7 B 347 TYR LEU THR ASP SER LEU ASP PRO ASN GLU LEU GLU ARG SEQRES 8 B 347 GLY PHE ASN GLU GLY VAL PHE THR ALA ALA KCX LEU TYR SEQRES 9 B 347 PRO ALA ASN ALA THR ALA ASN SER SER HIS GLY VAL THR SEQRES 10 B 347 SER VAL ASP ALA ILE MET PRO VAL LEU GLU ARG MET GLU SEQRES 11 B 347 LYS ILE GLY MET PRO LEU LEU VAL HIS GLY GLU VAL THR SEQRES 12 B 347 HIS ALA ASP ILE ASP ILE PHE ASP ARG GLU ALA ARG PHE SEQRES 13 B 347 ILE GLU SER VAL MET GLU PRO LEU ARG GLN ARG LEU THR SEQRES 14 B 347 ALA LEU LYS VAL VAL PHE GLU HIS ILE THR THR LYS ASP SEQRES 15 B 347 ALA ALA ASP TYR VAL ARG ASP GLY ASN GLU ARG LEU ALA SEQRES 16 B 347 ALA THR ILE THR PRO GLN HIS LEU MET PHE ASN ARG ASN SEQRES 17 B 347 HIS MET LEU VAL GLY GLY VAL ARG PRO HIS LEU TYR CYS SEQRES 18 B 347 LEU PRO ILE LEU LYS ARG ASN ILE HIS GLN GLN ALA LEU SEQRES 19 B 347 ARG GLU LEU VAL ALA SER GLY PHE ASN ARG VAL PHE LEU SEQRES 20 B 347 GLY THR ASP SER ALA PRO HIS ALA ARG HIS ARG LYS GLU SEQRES 21 B 347 SER SER CYS GLY CYS ALA GLY CYS PHE ASN ALA PRO THR SEQRES 22 B 347 ALA LEU GLY SER TYR ALA THR VAL PHE GLU GLU MET ASN SEQRES 23 B 347 ALA LEU GLN HIS PHE GLU ALA PHE CYS SER VAL ASN GLY SEQRES 24 B 347 PRO GLN PHE TYR GLY LEU PRO VAL ASN ASP THR PHE ILE SEQRES 25 B 347 GLU LEU VAL ARG GLU GLU GLN GLN VAL ALA GLU SER ILE SEQRES 26 B 347 ALA LEU THR ASP ASP THR LEU VAL PRO PHE LEU ALA GLY SEQRES 27 B 347 GLU THR VAL ARG TRP SER VAL LYS GLN
MODRES 2Z26 KCX A 102 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 2Z26 KCX B 102 LYS LYSINE NZ-CARBOXYLIC ACID
HET KCX A 102 12 HET KCX B 102 12 HET ZN A 400 1 HET ZN A 401 1 HET ZN B 400 1 HET ZN B 401 1 HET DOR A1410 11 HET NCD B1420 12 HET DOR B1430 11 HET MLI A1440 7
HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM ZN ZINC ION HETNAM DOR (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID HETNAM NCD N-CARBAMOYL-L-ASPARTATE HETNAM MLI MALONATE ION
HETSYN DOR DIHYDROOROTIC ACID
FORMUL 1 KCX 2(C7 H14 N2 O4) FORMUL 3 ZN 4(ZN 2+) FORMUL 7 DOR 2(C5 H6 N2 O4) FORMUL 8 NCD C5 H8 N2 O5 FORMUL 10 MLI C3 H2 O4 2- FORMUL 11 HOH *782(H2 O)
HELIX 1 1 ASP A 21 GLU A 34 1 14 HELIX 2 2 THR A 51 ALA A 65 1 15 HELIX 3 3 ASP A 85 GLU A 95 1 11 HELIX 4 4 SER A 118 ALA A 121 5 4 HELIX 5 5 ILE A 122 GLY A 133 1 12 HELIX 6 6 ASP A 148 PHE A 150 5 3 HELIX 7 7 ASP A 151 VAL A 160 1 10 HELIX 8 8 VAL A 160 LEU A 168 1 9 HELIX 9 9 THR A 180 ASP A 189 1 10 HELIX 10 10 THR A 199 PHE A 205 1 7 HELIX 11 11 ASN A 206 VAL A 212 1 7 HELIX 12 12 ARG A 216 TYR A 220 5 5 HELIX 13 13 ARG A 227 SER A 240 1 14 HELIX 14 14 ALA A 255 GLU A 260 1 6 HELIX 15 15 THR A 273 MET A 285 1 13 HELIX 16 16 ALA A 287 GLN A 289 5 3 HELIX 17 17 HIS A 290 VAL A 297 1 8 HELIX 18 18 VAL A 297 GLY A 304 1 8 HELIX 19 19 ASP B 21 GLU B 34 1 14 HELIX 20 20 THR B 51 ALA B 65 1 15 HELIX 21 21 ASP B 85 GLU B 95 1 11 HELIX 22 22 VAL B 119 ALA B 121 5 3 HELIX 23 23 ILE B 122 GLY B 133 1 12 HELIX 24 24 ASP B 148 PHE B 150 5 3 HELIX 25 25 ASP B 151 VAL B 160 1 10 HELIX 26 26 VAL B 160 LEU B 168 1 9 HELIX 27 27 THR B 180 ASP B 189 1 10 HELIX 28 28 THR B 199 PHE B 205 1 7 HELIX 29 29 ASN B 206 VAL B 212 1 7 HELIX 30 30 ARG B 216 TYR B 220 5 5 HELIX 31 31 ARG B 227 SER B 240 1 14 HELIX 32 32 ALA B 255 GLU B 260 1 6 HELIX 33 33 THR B 273 MET B 285 1 13 HELIX 34 34 ALA B 287 GLN B 289 5 3 HELIX 35 35 HIS B 290 VAL B 297 1 8 HELIX 36 36 VAL B 297 GLY B 304 1 8
SHEET 1 A 3 VAL A 6 ARG A 10 0 SHEET 2 A 3 PHE A 311 VAL A 315 -1 O LEU A 314 N LEU A 7 SHEET 3 A 3 SER A 344 VAL A 345 -1 O SER A 344 N VAL A 315 SHEET 1 B 8 ASP A 14 LEU A 17 0 SHEET 2 B 8 ARG A 38 VAL A 41 1 O ILE A 40 N LEU A 17 SHEET 3 B 8 THR A 73 TYR A 79 1 O LEU A 75 N ALA A 39 SHEET 4 B 8 PHE A 98 LEU A 103 1 O KCX A 102 N CYS A 78 SHEET 5 B 8 LEU A 136 VAL A 138 1 O LEU A 137 N ALA A 101 SHEET 6 B 8 VAL A 173 PHE A 175 1 O VAL A 174 N VAL A 138 SHEET 7 B 8 LEU A 194 ILE A 198 1 O ALA A 195 N PHE A 175 SHEET 8 B 8 VAL A 245 LEU A 247 1 O PHE A 246 N ALA A 196 SHEET 1 C 2 GLN A 319 GLN A 320 0 SHEET 2 C 2 THR A 340 VAL A 341 -1 O VAL A 341 N GLN A 319 SHEET 1 D 2 ILE A 325 ALA A 326 0 SHEET 2 D 2 THR A 331 LEU A 332 -1 O LEU A 332 N ILE A 325 SHEET 1 E 3 VAL B 6 ARG B 10 0 SHEET 2 E 3 PHE B 311 VAL B 315 -1 O LEU B 314 N LEU B 7 SHEET 3 E 3 SER B 344 VAL B 345 -1 O SER B 344 N VAL B 315 SHEET 1 F 8 ASP B 14 LEU B 17 0 SHEET 2 F 8 ARG B 38 VAL B 41 1 O ILE B 40 N ASP B 14 SHEET 3 F 8 THR B 73 TYR B 79 1 O LEU B 75 N ALA B 39 SHEET 4 F 8 PHE B 98 LEU B 103 1 O THR B 99 N MET B 76 SHEET 5 F 8 LEU B 136 VAL B 138 1 O LEU B 137 N LEU B 103 SHEET 6 F 8 VAL B 173 PHE B 175 1 O VAL B 174 N VAL B 138 SHEET 7 F 8 LEU B 194 ILE B 198 1 O ALA B 195 N PHE B 175 SHEET 8 F 8 VAL B 245 LEU B 247 1 O PHE B 246 N ALA B 196 SHEET 1 G 2 GLN B 319 GLN B 320 0 SHEET 2 G 2 THR B 340 VAL B 341 -1 O VAL B 341 N GLN B 319 SHEET 1 H 2 ILE B 325 ALA B 326 0 SHEET 2 H 2 THR B 331 LEU B 332 -1 O LEU B 332 N ILE B 325
LINK NE2 HIS A 16 ZN ZN A 401 1555 1555 2.09 LINK NE2 HIS A 18 ZN ZN A 401 1555 1555 2.07 LINK OQ2 KCX A 102 ZN ZN A 400 1555 1555 1.93 LINK OQ1 KCX A 102 ZN ZN A 401 1555 1555 2.16 LINK ND1 HIS A 139 ZN ZN A 400 1555 1555 2.06 LINK NE2 HIS A 177 ZN ZN A 400 1555 1555 2.04 LINK OD1 ASP A 250 ZN ZN A 401 1555 1555 2.12 LINK NE2 HIS B 16 ZN ZN B 401 1555 1555 2.10 LINK NE2 HIS B 18 ZN ZN B 401 1555 1555 2.05 LINK OQ2 KCX B 102 ZN ZN B 400 1555 1555 1.91 LINK OQ1 KCX B 102 ZN ZN B 401 1555 1555 2.15 LINK ND1 HIS B 139 ZN ZN B 400 1555 1555 2.05 LINK NE2 HIS B 177 ZN ZN B 400 1555 1555 2.04 LINK OD1 ASP B 250 ZN ZN B 401 1555 1555 2.12
CISPEP 1 ALA A 46 PRO A 47 0 2.94 CISPEP 2 LEU A 222 PRO A 223 0 -2.32 CISPEP 3 ALA B 46 PRO B 47 0 1.43 CISPEP 4 LEU B 222 PRO B 223 0 -5.58
SITE 1 AC1 6 KCX A 102 HIS A 139 HIS A 177 ZN A 401 SITE 2 AC1 6 DOR A1410 HOH A1441 SITE 1 AC2 6 HIS A 16 HIS A 18 KCX A 102 ASP A 250 SITE 2 AC2 6 ZN A 400 HOH A1441 SITE 1 AC3 7 KCX B 102 HIS B 139 HIS B 177 ZN B 401 SITE 2 AC3 7 NCD B1420 DOR B1430 HOH B1431 SITE 1 AC4 7 HIS B 16 HIS B 18 KCX B 102 ASP B 250 SITE 2 AC4 7 ZN B 400 NCD B1420 HOH B1431 SITE 1 AC5 14 HIS A 18 ARG A 20 ASN A 44 HIS A 139 SITE 2 AC5 14 CYS A 221 LEU A 222 ALA A 252 HIS A 254 SITE 3 AC5 14 ALA A 266 GLY A 267 ZN A 400 HOH A1441 SITE 4 AC5 14 HOH A1718 HOH A1779 SITE 1 AC6 17 HIS B 16 HIS B 18 ARG B 20 ASN B 44 SITE 2 AC6 17 KCX B 102 HIS B 139 HIS B 177 CYS B 221 SITE 3 AC6 17 LEU B 222 ASP B 250 ALA B 252 HIS B 254 SITE 4 AC6 17 ALA B 266 GLY B 267 ZN B 400 ZN B 401 SITE 5 AC6 17 HOH B1431 SITE 1 AC7 12 HIS B 18 ARG B 20 ASN B 44 HIS B 139 SITE 2 AC7 12 CYS B 221 LEU B 222 ALA B 252 HIS B 254 SITE 3 AC7 12 ALA B 266 GLY B 267 ZN B 400 HOH B1431 SITE 1 AC8 9 ARG A 207 ARG A 227 HOH A1443 HOH A1578 SITE 2 AC8 9 PHE B 150 ARG B 207 ARG B 227 HOH B1570 SITE 3 AC8 9 HOH B1707
CRYST1 51.493 78.885 180.091 90.00 90.00 90.00 P 21 21 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 0.019420 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012677 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005553 0.00000