HEADER OXIDOREDUCTASE 19-DEC-01 1KNP TITLE E. COLI L-ASPARTATE OXIDASE: MUTANT R386L IN COMPLEX WITH SUCCINATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-ASPARTATE OXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.4.3.16; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NADB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS FUMARATE REDUCTASE FAMILY OF OXIDOREDUCTASES, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.T.BOSSI,A.MATTEVI REVDAT 5 29-MAY-24 1KNP 1 REMARK REVDAT 4 10-NOV-21 1KNP 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1KNP 1 VERSN REVDAT 2 04-DEC-02 1KNP 1 REMARK REVDAT 1 17-APR-02 1KNP 0 JRNL AUTH R.T.BOSSI,A.NEGRI,G.TEDESCHI,A.MATTEVI JRNL TITL STRUCTURE OF FAD-BOUND L-ASPARTATE OXIDASE: INSIGHT INTO JRNL TITL 2 SUBSTRATE SPECIFICITY AND CATALYSIS. JRNL REF BIOCHEMISTRY V. 41 3018 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11863440 JRNL DOI 10.1021/BI015939R REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 23396 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1262 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1649 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4150 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 20 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.46000 REMARK 3 B22 (A**2) : 3.46000 REMARK 3 B33 (A**2) : -6.92000 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): 0.505 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.324 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.273 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.920 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4309 ; 0.025 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5864 ; 2.540 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 528 ; 5.304 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 725 ;20.759 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 649 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3302 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2291 ; 0.334 ; 0.300 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): 340 ; 0.252 ; 0.500 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): 30 ; 0.444 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.321 ; 0.500 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): 2627 ; 1.049 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4230 ; 1.937 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1682 ; 3.161 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1634 ; 4.937 ; 4.500 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22099 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : 0.11600 REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.37700 REMARK 200 R SYM FOR SHELL (I) : 0.37700 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ISPROPANOL, HEPES, SODIUM CITRATE, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 154.56000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.27000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.27000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.28000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.27000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.27000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 231.84000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.27000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.27000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.28000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.27000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.27000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 231.84000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 154.56000 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: MONOMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 THR A 3 REMARK 465 LEU A 4 REMARK 465 GLY A 534 REMARK 465 ASN A 535 REMARK 465 HIS A 536 REMARK 465 TYR A 537 REMARK 465 ILE A 538 REMARK 465 ASN A 539 REMARK 465 ARG A 540 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 425 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 NA NA A 541 O HOH A 812 0.90 REMARK 500 O ARG A 91 N GLN A 95 1.47 REMARK 500 N ARG A 91 O HOH A 818 1.88 REMARK 500 O TYR A 478 NH2 ARG A 491 1.93 REMARK 500 O ALA A 90 N CYS A 93 2.04 REMARK 500 O ALA A 90 N VAL A 94 2.05 REMARK 500 O ARG A 91 CB GLN A 95 2.15 REMARK 500 N HIS A 107 O SER A 115 2.16 REMARK 500 O ARG A 91 CA GLN A 95 2.16 REMARK 500 O SER A 314 N LYS A 316 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 OE2 GLU A 283 CE1 HIS A 362 6465 2.03 REMARK 500 OE2 GLU A 432 NH2 ARG A 462 7556 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL A 210 CB VAL A 210 CG1 -0.141 REMARK 500 GLU A 424 CD GLU A 424 OE2 0.076 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 LEU A 25 CA - CB - CG ANGL. DEV. = -14.1 DEGREES REMARK 500 ASP A 64 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 79 CB - CG - OD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 105 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 PRO A 110 N - CA - C ANGL. DEV. = -15.8 DEGREES REMARK 500 ASP A 164 CB - CG - OD2 ANGL. DEV. = 9.2 DEGREES REMARK 500 ASP A 169 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 VAL A 210 CB - CA - C ANGL. DEV. = -13.5 DEGREES REMARK 500 ASP A 273 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 280 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 MET A 358 CG - SD - CE ANGL. DEV. = -12.3 DEGREES REMARK 500 ARG A 408 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 431 CB - CG - OD2 ANGL. DEV. = 8.7 DEGREES REMARK 500 ILE A 436 CG1 - CB - CG2 ANGL. DEV. = -19.8 DEGREES REMARK 500 LEU A 445 CB - CG - CD2 ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 462 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 GLU A 6 -76.37 -66.86 REMARK 500 GLN A 50 -69.84 -92.23 REMARK 500 PHE A 85 -73.11 -38.59 REMARK 500 ALA A 90 -89.75 -54.71 REMARK 500 ASP A 99 0.05 -63.83 REMARK 500 ASP A 105 112.19 -38.29 REMARK 500 HIS A 107 -135.58 -83.78 REMARK 500 ILE A 108 -16.89 -173.18 REMARK 500 GLN A 109 40.99 -161.24 REMARK 500 PRO A 110 177.61 -49.85 REMARK 500 ARG A 128 34.06 -150.08 REMARK 500 ALA A 133 -137.75 44.65 REMARK 500 ALA A 135 51.57 -145.57 REMARK 500 ARG A 159 54.38 36.42 REMARK 500 SER A 220 56.49 -65.40 REMARK 500 ASN A 255 97.50 -163.16 REMARK 500 THR A 259 151.99 -48.15 REMARK 500 CYS A 308 -173.47 -179.87 REMARK 500 HIS A 315 0.57 -49.09 REMARK 500 ALA A 318 -46.96 -25.96 REMARK 500 PRO A 326 -74.14 -50.84 REMARK 500 ASP A 360 -159.31 -94.97 REMARK 500 ASN A 385 117.56 -174.23 REMARK 500 ILE A 416 93.94 -63.06 REMARK 500 ASP A 423 50.07 -66.82 REMARK 500 GLU A 424 109.52 -18.24 REMARK 500 ASN A 429 87.15 -179.84 REMARK 500 VAL A 451 44.29 -144.96 REMARK 500 LYS A 508 41.49 -78.22 REMARK 500 TYR A 519 73.34 -156.97 REMARK 500 SER A 526 -165.76 -113.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 108 GLN A 109 -149.67 REMARK 500 REMARK 500 REMARK: NULL 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 NA A 541 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 353 O REMARK 620 2 GLY A 355 O 77.6 REMARK 620 3 GLU A 375 O 106.0 119.2 REMARK 620 4 SER A 377 O 143.7 77.9 109.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 541 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SIN A 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CHU RELATED DB: PDB REMARK 900 1CHU CONTAINS L-ASPARTATE OXIDASE, WILD-TYPE IN APOFORM REMARK 900 RELATED ID: 1KNR RELATED DB: PDB REMARK 900 1KNR CONTAINS L-ASPARTATE OXIDASE, R386L MUTANT DBREF 1KNP A 1 540 UNP P10902 NADB_ECOLI 1 540 SEQADV 1KNP LEU A 386 UNP P10902 ARG 386 ENGINEERED MUTATION SEQRES 1 A 540 MET ASN THR LEU PRO GLU HIS SER CYS ASP VAL LEU ILE SEQRES 2 A 540 ILE GLY SER GLY ALA ALA GLY LEU SER LEU ALA LEU ARG SEQRES 3 A 540 LEU ALA ASP GLN HIS GLN VAL ILE VAL LEU SER LYS GLY SEQRES 4 A 540 PRO VAL THR GLU GLY SER THR PHE TYR ALA GLN GLY GLY SEQRES 5 A 540 ILE ALA ALA VAL PHE ASP GLU THR ASP SER ILE ASP SER SEQRES 6 A 540 HIS VAL GLU ASP THR LEU ILE ALA GLY ALA GLY ILE CYS SEQRES 7 A 540 ASP ARG HIS ALA VAL GLU PHE VAL ALA SER ASN ALA ARG SEQRES 8 A 540 SER CYS VAL GLN TRP LEU ILE ASP GLN GLY VAL LEU PHE SEQRES 9 A 540 ASP THR HIS ILE GLN PRO ASN GLY GLU GLU SER TYR HIS SEQRES 10 A 540 LEU THR ARG GLU GLY GLY HIS SER HIS ARG ARG ILE LEU SEQRES 11 A 540 HIS ALA ALA ASP ALA THR GLY ARG GLU VAL GLU THR THR SEQRES 12 A 540 LEU VAL SER LYS ALA LEU ASN HIS PRO ASN ILE ARG VAL SEQRES 13 A 540 LEU GLU ARG THR ASN ALA VAL ASP LEU ILE VAL SER ASP SEQRES 14 A 540 LYS ILE GLY LEU PRO GLY THR ARG ARG VAL VAL GLY ALA SEQRES 15 A 540 TRP VAL TRP ASN ARG ASN LYS GLU THR VAL GLU THR CYS SEQRES 16 A 540 HIS ALA LYS ALA VAL VAL LEU ALA THR GLY GLY ALA SER SEQRES 17 A 540 LYS VAL TYR GLN TYR THR THR ASN PRO ASP ILE SER SER SEQRES 18 A 540 GLY ASP GLY ILE ALA MET ALA TRP ARG ALA GLY CYS ARG SEQRES 19 A 540 VAL ALA ASN LEU GLU PHE ASN GLN PHE HIS PRO THR ALA SEQRES 20 A 540 LEU TYR HIS PRO GLN ALA ARG ASN PHE LEU LEU THR GLU SEQRES 21 A 540 ALA LEU ARG GLY GLU GLY ALA TYR LEU LYS ARG PRO ASP SEQRES 22 A 540 GLY THR ARG PHE MET PRO ASP PHE ASP GLU ARG GLY GLU SEQRES 23 A 540 LEU ALA PRO ARG ASP ILE VAL ALA ARG ALA ILE ASP HIS SEQRES 24 A 540 GLU MET LYS ARG LEU GLY ALA ASP CYS MET PHE LEU ASP SEQRES 25 A 540 ILE SER HIS LYS PRO ALA ASP PHE ILE ARG GLN HIS PHE SEQRES 26 A 540 PRO MET ILE TYR GLU LYS LEU LEU GLY LEU GLY ILE ASP SEQRES 27 A 540 LEU THR GLN GLU PRO VAL PRO ILE VAL PRO ALA ALA HIS SEQRES 28 A 540 TYR THR CYS GLY GLY VAL MET VAL ASP ASP HIS GLY ARG SEQRES 29 A 540 THR ASP VAL GLU GLY LEU TYR ALA ILE GLY GLU VAL SER SEQRES 30 A 540 TYR THR GLY LEU HIS GLY ALA ASN LEU MET ALA SER ASN SEQRES 31 A 540 SER LEU LEU GLU CYS LEU VAL TYR GLY TRP SER ALA ALA SEQRES 32 A 540 GLU ASP ILE THR ARG ARG MET PRO TYR ALA HIS ASP ILE SEQRES 33 A 540 SER THR LEU PRO PRO TRP ASP GLU SER ARG VAL GLU ASN SEQRES 34 A 540 PRO ASP GLU ARG VAL VAL ILE GLN HIS ASN TRP HIS GLU SEQRES 35 A 540 LEU ARG LEU PHE MET TRP ASP TYR VAL GLY ILE VAL ARG SEQRES 36 A 540 THR THR LYS ARG LEU GLU ARG ALA LEU ARG ARG ILE THR SEQRES 37 A 540 MET LEU GLN GLN GLU ILE ASP GLU TYR TYR ALA HIS PHE SEQRES 38 A 540 ARG VAL SER ASN ASN LEU LEU GLU LEU ARG ASN LEU VAL SEQRES 39 A 540 GLN VAL ALA GLU LEU ILE VAL ARG CYS ALA MET MET ARG SEQRES 40 A 540 LYS GLU SER ARG GLY LEU HIS PHE THR LEU ASP TYR PRO SEQRES 41 A 540 GLU LEU LEU THR HIS SER GLY PRO SER ILE LEU SER PRO SEQRES 42 A 540 GLY ASN HIS TYR ILE ASN ARG HET NA A 541 1 HET FAD A 800 53 HET SIN A 801 8 HETNAM NA SODIUM ION HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM SIN SUCCINIC ACID FORMUL 2 NA NA 1+ FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 SIN C4 H6 O4 FORMUL 5 HOH *20(H2 O) HELIX 1 1 GLY A 17 ASP A 29 1 13 HELIX 2 2 GLY A 44 ALA A 49 5 6 HELIX 3 3 SER A 62 GLY A 74 1 13 HELIX 4 4 ASP A 79 SER A 88 1 10 HELIX 5 5 ASN A 89 ASP A 99 1 11 HELIX 6 6 ALA A 135 ASN A 150 1 16 HELIX 7 7 ASP A 169 ILE A 171 5 3 HELIX 8 8 ALA A 207 TYR A 211 5 5 HELIX 9 9 GLY A 222 ALA A 231 1 10 HELIX 10 10 THR A 259 GLU A 265 1 7 HELIX 11 11 PHE A 277 PHE A 281 5 5 HELIX 12 12 ARG A 284 ALA A 288 5 5 HELIX 13 13 PRO A 289 GLY A 305 1 17 HELIX 14 14 PRO A 317 PHE A 325 1 9 HELIX 15 15 PHE A 325 GLY A 334 1 10 HELIX 16 16 ASN A 390 MET A 410 1 21 HELIX 17 17 PRO A 411 ALA A 413 5 3 HELIX 18 18 ASN A 429 VAL A 451 1 23 HELIX 19 19 THR A 456 TYR A 478 1 23 HELIX 20 20 SER A 484 ARG A 507 1 24 SHEET 1 A 4 HIS A 7 SER A 8 0 SHEET 2 A 4 VAL A 192 HIS A 196 1 O HIS A 196 N HIS A 7 SHEET 3 A 4 VAL A 179 ASN A 186 -1 N VAL A 184 O GLU A 193 SHEET 4 A 4 THR A 160 VAL A 167 -1 N ILE A 166 O VAL A 180 SHEET 1 B 5 ILE A 154 LEU A 157 0 SHEET 2 B 5 VAL A 33 LEU A 36 1 N VAL A 33 O ARG A 155 SHEET 3 B 5 VAL A 11 ILE A 14 1 N ILE A 13 O LEU A 36 SHEET 4 B 5 ALA A 199 LEU A 202 1 O ALA A 199 N LEU A 12 SHEET 5 B 5 LEU A 370 ALA A 372 1 O TYR A 371 N VAL A 200 SHEET 1 C 3 ILE A 53 ALA A 54 0 SHEET 2 C 3 ILE A 129 LEU A 130 -1 O LEU A 130 N ILE A 53 SHEET 3 C 3 LEU A 118 THR A 119 -1 N THR A 119 O ILE A 129 SHEET 1 D 4 SER A 377 TYR A 378 0 SHEET 2 D 4 GLY A 356 MET A 358 1 N VAL A 357 O TYR A 378 SHEET 3 D 4 VAL A 235 ALA A 236 -1 N ALA A 236 O GLY A 356 SHEET 4 D 4 ILE A 530 LEU A 531 -1 O LEU A 531 N VAL A 235 SHEET 1 E 4 ASN A 241 LEU A 248 0 SHEET 2 E 4 VAL A 344 THR A 353 -1 O VAL A 347 N ALA A 247 SHEET 3 E 4 MET A 309 ASP A 312 -1 N LEU A 311 O VAL A 344 SHEET 4 E 4 TYR A 268 LYS A 270 -1 N TYR A 268 O ASP A 312 LINK O THR A 353 NA NA A 541 1555 1555 2.53 LINK O GLY A 355 NA NA A 541 1555 1555 2.26 LINK O GLU A 375 NA NA A 541 1555 1555 1.98 LINK O SER A 377 NA NA A 541 1555 1555 2.26 SITE 1 AC1 5 THR A 353 GLY A 355 GLU A 375 SER A 377 SITE 2 AC1 5 HOH A 812 SITE 1 AC2 32 GLY A 15 SER A 16 GLY A 17 ALA A 18 SITE 2 AC2 32 ALA A 19 SER A 37 LYS A 38 SER A 45 SITE 3 AC2 32 THR A 46 TYR A 48 ALA A 49 GLN A 50 SITE 4 AC2 32 GLY A 51 GLY A 52 THR A 160 ASN A 161 SITE 5 AC2 32 ALA A 162 ALA A 203 THR A 204 GLY A 205 SITE 6 AC2 32 ASN A 216 ASP A 223 LEU A 257 HIS A 351 SITE 7 AC2 32 TYR A 352 GLY A 374 GLU A 375 SER A 389 SITE 8 AC2 32 SER A 391 LEU A 392 CYS A 395 SIN A 801 SITE 1 AC3 11 GLY A 51 GLU A 121 HIS A 244 THR A 259 SITE 2 AC3 11 GLU A 260 ARG A 290 HIS A 351 ALA A 388 SITE 3 AC3 11 SER A 389 SER A 391 FAD A 800 CRYST1 72.540 72.540 309.120 90.00 90.00 90.00 P 41 21 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 0.013785 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003235 0.00000