HEADER OXIDOREDUCTASE 01-MAY-14 4D13 TITLE CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE IN COMPLEX WITH ITS TITLE 2 5-PEROXOISOURATE INTERMEDIATE (X-RAY DOSE, 2.2 KGY) COMPND MOL_ID: 1; COMPND 2 MOLECULE: URICASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: URATE OXIDASE; COMPND 5 EC: 1.7.3.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS FLAVUS; SOURCE 3 ORGANISM_TAXID: 5059; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, COFACTOR-FREE OXIDASE EXPDTA X-RAY DIFFRACTION AUTHOR S.BUI,R.A.STEINER REVDAT 4 21-FEB-18 4D13 1 JRNL REVDAT 3 13-DEC-17 4D13 1 JRNL REVDAT 2 17-DEC-14 4D13 1 JRNL REVDAT 1 29-OCT-14 4D13 0 JRNL AUTH S.BUI,D.VON STETTEN,P.G.JAMBRINA,T.PRANGE,N.COLLOC'H, JRNL AUTH 2 D.DE SANCTIS,A.ROYANT,E.ROSTA,R.A.STEINER JRNL TITL DIRECT EVIDENCE FOR A PEROXIDE INTERMEDIATE AND A REACTIVE JRNL TITL 2 ENZYME-SUBSTRATE-DIOXYGEN CONFIGURATION IN A COFACTOR-FREE JRNL TITL 3 OXIDASE. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 53 13710 2014 JRNL REFN ESSN 1521-3773 JRNL PMID 25314114 JRNL DOI 10.1002/ANIE.201405485 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 91916 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) : 0.109 REMARK 3 R VALUE (WORKING SET) : 0.108 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4841 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6671 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 355 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 637 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : -0.44000 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): 0.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.170 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2723 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2578 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3750 ; 1.447 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5985 ; 0.770 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 417 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3202 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 640 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1297 ; 1.085 ; 0.976 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1296 ; 1.110 ; 0.979 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1647 ; 1.377 ; 1.475 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1426 ; 1.599 ; 1.177 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5301 ; 1.823 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 147 ;37.910 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5699 ; 8.716 ; 5.000 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 : 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 RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 4D13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96758 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MG/ML UOX IN 50 MM TRIS-ACETATE PH REMARK 280 8.0 SATURATED WITH 9-METHYL URIC ACID UNDER ANAEROBIC CONDITIONS REMARK 280 RESERVOIR: 8% PEG 8000, 50 MM TRIS-ACETATE PH 8.0 REMARK 280 CRYSTALLIZATION WAS CARRIED OUT ANAEROBICALLY. CRYSTALS WERE REMARK 280 INCUBATED WITH A RESERVOIR SOLUTION ENRICHED BY 10 MM H2O2 AND REMARK 280 20% GLYCEROL TO GENERATE THE PEROXIDE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 39.96500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.54000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.03000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.96500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.54000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.03000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.96500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.54000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.03000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.96500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.54000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.03000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 25470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 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 79.93000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 104.06000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 79.93000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 95.08000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 95.08000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 104.06000 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 HOH A2145 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2302 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 0 REMARK 465 LEU A 297 REMARK 465 LYS A 298 REMARK 465 SER A 299 REMARK 465 LYS A 300 REMARK 465 LEU A 301 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 SER A 296 CA C O CB OG 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 O HOH A 2330 O HOH A 2333 2.06 REMARK 500 OE1 GLN A 187 O HOH A 2464 2.13 REMARK 500 OE1 GLN A 131 O HOH A 2358 2.14 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 2340 O HOH A 2384 4566 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 A 118 28.01 -153.20 REMARK 500 SER A 124 167.25 90.57 REMARK 500 ASP A 175 105.89 -163.12 REMARK 500 SER A 226 163.41 179.39 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 A2073 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A2120 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A2122 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A2127 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A2176 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A2222 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A2229 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A2439 DISTANCE = 13.04 ANGSTROMS REMARK 525 HOH A2508 DISTANCE = 22.56 ANGSTROMS REMARK 525 HOH A3005 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A3017 DISTANCE = 10.76 ANGSTROMS REMARK 525 HOH A3035 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A3041 DISTANCE = 22.32 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IUP A 1297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1298 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D12 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE ANAEROBICALLY REMARK 900 COMPLEXED WITH URIC ACID REMARK 900 RELATED ID: 4D17 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE IN COMPLEX WITH REMARK 900 ITS 5-PEROXOISOURATE INTERMEDIATE (X-RAY DOSE, 106 KGY) REMARK 900 RELATED ID: 4D19 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE IN COMPLEX WITH REMARK 900 ITS 5-PEROXOISOURATE INTERMEDIATE (X-RAY DOSE, 1.75 MGY) DBREF 4D13 A 0 301 UNP Q00511 URIC_ASPFL 1 302 SEQRES 1 A 302 MET SER ALA VAL LYS ALA ALA ARG TYR GLY LYS ASP ASN SEQRES 2 A 302 VAL ARG VAL TYR LYS VAL HIS LYS ASP GLU LYS THR GLY SEQRES 3 A 302 VAL GLN THR VAL TYR GLU MET THR VAL CYS VAL LEU LEU SEQRES 4 A 302 GLU GLY GLU ILE GLU THR SER TYR THR LYS ALA ASP ASN SEQRES 5 A 302 SER VAL ILE VAL ALA THR ASP SER ILE LYS ASN THR ILE SEQRES 6 A 302 TYR ILE THR ALA LYS GLN ASN PRO VAL THR PRO PRO GLU SEQRES 7 A 302 LEU PHE GLY SER ILE LEU GLY THR HIS PHE ILE GLU LYS SEQRES 8 A 302 TYR ASN HIS ILE HIS ALA ALA HIS VAL ASN ILE VAL CYS SEQRES 9 A 302 HIS ARG TRP THR ARG MET ASP ILE ASP GLY LYS PRO HIS SEQRES 10 A 302 PRO HIS SER PHE ILE ARG ASP SER GLU GLU LYS ARG ASN SEQRES 11 A 302 VAL GLN VAL ASP VAL VAL GLU GLY LYS GLY ILE ASP ILE SEQRES 12 A 302 LYS SER SER LEU SER GLY LEU THR VAL LEU LYS SER THR SEQRES 13 A 302 ASN SER GLN PHE TRP GLY PHE LEU ARG ASP GLU TYR THR SEQRES 14 A 302 THR LEU LYS GLU THR TRP ASP ARG ILE LEU SER THR ASP SEQRES 15 A 302 VAL ASP ALA THR TRP GLN TRP LYS ASN PHE SER GLY LEU SEQRES 16 A 302 GLN GLU VAL ARG SER HIS VAL PRO LYS PHE ASP ALA THR SEQRES 17 A 302 TRP ALA THR ALA ARG GLU VAL THR LEU LYS THR PHE ALA SEQRES 18 A 302 GLU ASP ASN SER ALA SER VAL GLN ALA THR MET TYR LYS SEQRES 19 A 302 MET ALA GLU GLN ILE LEU ALA ARG GLN GLN LEU ILE GLU SEQRES 20 A 302 THR VAL GLU TYR SER LEU PRO ASN LYS HIS TYR PHE GLU SEQRES 21 A 302 ILE ASP LEU SER TRP HIS LYS GLY LEU GLN ASN THR GLY SEQRES 22 A 302 LYS ASN ALA GLU VAL PHE ALA PRO GLN SER ASP PRO ASN SEQRES 23 A 302 GLY LEU ILE LYS CYS THR VAL GLY ARG SER SER LEU LYS SEQRES 24 A 302 SER LYS LEU HET IUP A1297 14 HET MPD A1298 8 HETNAM IUP 5-(HYDRO)PEROXOISOURATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 IUP C5 H4 N4 O5 FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *637(H2 O) HELIX 1 1 ILE A 42 LYS A 48 1 7 HELIX 2 2 ASP A 50 ILE A 54 5 5 HELIX 3 3 ALA A 56 ASN A 71 1 16 HELIX 4 4 PRO A 75 TYR A 91 1 17 HELIX 5 5 GLY A 193 HIS A 200 1 8 HELIX 6 6 HIS A 200 ASP A 222 1 23 HELIX 7 7 SER A 226 GLN A 242 1 17 HELIX 8 8 THR A 271 ALA A 275 5 5 SHEET 1 AA 8 TYR A 8 LYS A 20 0 SHEET 2 AA 8 GLN A 27 GLY A 40 -1 O THR A 28 N HIS A 19 SHEET 3 AA 8 ILE A 94 HIS A 104 -1 N HIS A 95 O GLU A 39 SHEET 4 AA 8 LYS A 127 VAL A 135 -1 O ARG A 128 N CYS A 103 SHEET 5 AA 8 ILE A 140 LYS A 153 -1 O ASP A 141 N ASP A 133 SHEET 6 AA 8 LEU A 178 TRP A 188 -1 O LEU A 178 N LYS A 153 SHEET 7 AA 8 ILE A 245 ASN A 254 -1 N GLU A 246 O GLN A 187 SHEET 8 AA 8 GLY A 286 GLY A 293 -1 O GLY A 286 N ASN A 254 SHEET 1 AB 2 THR A 107 ILE A 111 0 SHEET 2 AB 2 LYS A 114 ILE A 121 -1 O LYS A 114 N ILE A 111 SHEET 1 AC 2 TYR A 257 GLU A 259 0 SHEET 2 AC 2 PHE A 278 PRO A 280 -1 O ALA A 279 N PHE A 258 CISPEP 1 THR A 74 PRO A 75 0 -16.52 CISPEP 2 THR A 74 PRO A 75 0 -14.08 CISPEP 3 ASP A 283 PRO A 284 0 -9.95 CISPEP 4 ASP A 283 PRO A 284 0 -12.19 SITE 1 AC1 15 ILE A 54 ALA A 56 THR A 57 ASP A 58 SITE 2 AC1 15 PHE A 159 LEU A 170 ARG A 176 SER A 226 SITE 3 AC1 15 VAL A 227 GLN A 228 ASN A 254 HIS A 256 SITE 4 AC1 15 GLY A 286 ILE A 288 HOH A2449 SITE 1 AC2 4 GLN A 158 TRP A 174 HOH A2474 HOH A2526 CRYST1 79.930 95.080 104.060 90.00 90.00 90.00 I 2 2 2 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 0.012511 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009610 0.00000