HEADER OXIDOREDUCTASE 21-FEB-20 6Y4J TITLE ENGINEERED FRUCTOSYL PEPTIDE OXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRUCTOSYL PEPTIDE OXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DONINI,F.RIGOLDI,A.GAUTIERI,E.PARISINI REVDAT 4 13-NOV-24 6Y4J 1 REMARK REVDAT 3 24-JAN-24 6Y4J 1 REMARK REVDAT 2 03-MAR-21 6Y4J 1 JRNL REVDAT 1 13-JAN-21 6Y4J 0 JRNL AUTH F.RIGOLDI,S.DONINI,A.TORRETTA,A.CARBONE,A.REDAELLI, JRNL AUTH 2 T.BANDIERA,E.PARISINI,A.GAUTIERI JRNL TITL RATIONAL BACKBONE REDESIGN OF A FRUCTOSYL PEPTIDE OXIDASE TO JRNL TITL 2 WIDEN ITS ACTIVE SITE ACCESS TUNNEL. JRNL REF BIOTECHNOL.BIOENG. V. 117 3688 2020 JRNL REFN ESSN 1097-0290 JRNL PMID 32797625 JRNL DOI 10.1002/BIT.27535 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 105505 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5594 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7662 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.1650 REMARK 3 BIN FREE R VALUE SET COUNT : 425 REMARK 3 BIN FREE R VALUE : 0.2000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3336 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 669 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.14000 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): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.047 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.608 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3503 ; 0.017 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3179 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4757 ; 2.082 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7381 ; 1.536 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 7.004 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;29.214 ;22.191 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 559 ;11.687 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.910 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3918 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 750 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : NULL 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 6Y4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106769. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118634 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 45.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.8000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.900 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: 5T1E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE PH 6.5, 12% PEG REMARK 280 20 K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 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 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.01650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.01650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.71750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.01650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.01650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.71750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.01650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.01650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.71750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.01650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.01650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.71750 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 A 602 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 772 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 808 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1220 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 HIS A 427 REMARK 465 HIS A 428 REMARK 465 HIS A 429 REMARK 465 HIS A 430 REMARK 465 HIS A 431 REMARK 465 HIS A 432 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 1043 O HOH A 1211 2.16 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 NH2 ARG A 201 NH2 ARG A 201 7555 2.08 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 SER A 48 CB SER A 48 OG -0.109 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 5 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 89 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 409 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 409 NE - CZ - NH2 ANGL. DEV. = -8.7 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 TRP A 112 -123.76 -104.45 REMARK 500 LEU A 114 145.36 66.17 REMARK 500 ASP A 115 -79.72 -92.95 REMARK 500 ALA A 116 -58.12 53.98 REMARK 500 TYR A 176 -135.07 60.44 REMARK 500 ALA A 210 56.08 -111.51 REMARK 500 VAL A 256 -55.42 -124.87 REMARK 500 THR A 307 -123.73 -119.49 REMARK 500 MET A 324 58.34 -140.37 REMARK 500 THR A 363 -155.45 -154.60 REMARK 500 ASP A 368 31.69 -143.88 REMARK 500 ARG A 399 57.04 -152.59 REMARK 500 SER A 408 -142.04 52.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 DBREF 6Y4J A 1 432 PDB 6Y4J 6Y4J 1 432 SEQRES 1 A 432 MET ALA PRO SER ARG ALA ASN THR LYS VAL ILE VAL VAL SEQRES 2 A 432 GLY GLY GLY GLY THR ILE GLY SER SER THR ALA LEU HIS SEQRES 3 A 432 LEU VAL ARG SER GLY TYR THR PRO SER ASN VAL THR VAL SEQRES 4 A 432 LEU ASP ALA TYR PRO ILE PRO SER SER GLN SER ALA GLY SEQRES 5 A 432 ASN ASP LEU ASN LYS ILE MET ASP ALA ASP ALA ASP PRO SEQRES 6 A 432 ALA ALA ASP ALA ALA ARG GLN MET TRP ASN GLU ASP GLU SEQRES 7 A 432 LEU PHE LYS LYS PHE PHE HIS ASN THR GLY ARG LEU ASP SEQRES 8 A 432 CYS ALA HIS GLY GLU LYS ASP ILE ALA ASP LEU LYS LYS SEQRES 9 A 432 ARG TYR GLN ASN LEU VAL ASP TRP GLY LEU ASP ALA THR SEQRES 10 A 432 VAL GLU TRP LEU ASP SER GLU ASP GLU ILE LEU LYS ARG SEQRES 11 A 432 MET PRO GLN LEU THR ARG ASP GLN ILE LYS GLY TRP LYS SEQRES 12 A 432 ALA ILE PHE SER LYS ASP GLY GLY TRP LEU ALA ALA ALA SEQRES 13 A 432 LYS ALA ILE LYS ALA ILE GLY GLU TYR LEU ARG ASP GLN SEQRES 14 A 432 GLY VAL ARG PHE GLY PHE TYR GLY ALA GLY SER PHE LYS SEQRES 15 A 432 GLN PRO LEU LEU ALA GLU GLY VAL CYS ILE GLY VAL GLU SEQRES 16 A 432 THR VAL ASP GLY THR ARG TYR TYR ALA ASP LYS VAL VAL SEQRES 17 A 432 LEU ALA ALA GLY ALA TRP SER PRO THR LEU VAL GLU LEU SEQRES 18 A 432 GLN GLU GLN CYS VAL SER LYS ALA TRP VAL TYR GLY HIS SEQRES 19 A 432 ILE GLN LEU THR PRO GLU GLU ALA ALA ARG TYR LYS ASN SEQRES 20 A 432 SER PRO VAL VAL TYR ASN GLY ASP VAL GLY PHE PHE PHE SEQRES 21 A 432 GLU PRO ASN GLU HIS GLY ILE ILE LYS VAL CYS ASP GLU SEQRES 22 A 432 PHE PRO GLY PHE THR ARG PHE LYS MET HIS GLN PRO PHE SEQRES 23 A 432 GLY ALA LYS ALA PRO LYS ARG ILE SER VAL PRO ARG SER SEQRES 24 A 432 HIS ALA LYS HIS PRO THR ASP THR ILE PRO ASP ALA SER SEQRES 25 A 432 ILE VAL ARG ILE ARG ARG ALA ILE ALA THR PHE MET PRO SEQRES 26 A 432 GLN PHE LYS ASN LYS PRO LEU PHE ASN GLN ALA MET CYS SEQRES 27 A 432 TRP CYS THR ASP THR ALA ASP GLY HIS LEU LEU ILE CYS SEQRES 28 A 432 GLU HIS PRO GLU TRP LYS ASN PHE TYR LEU ALA THR GLY SEQRES 29 A 432 ASP SER GLY ASP SER PHE LYS LEU LEU PRO ILE ILE GLY SEQRES 30 A 432 LYS TYR VAL VAL GLU LEU LEU GLU GLY THR LEU ALA ASP SEQRES 31 A 432 GLU LEU ALA HIS LYS TRP ARG TRP ARG PRO GLY SER GLY SEQRES 32 A 432 ASP ALA LEU LYS SER ARG ARG GLU ALA PRO ALA LYS ASP SEQRES 33 A 432 LEU ALA ASP MET PRO GLY TRP ASN HIS ASP HIS HIS HIS SEQRES 34 A 432 HIS HIS HIS HET FAD A 501 53 HET SO4 A 502 5 HET GOL A 503 6 HET GOL A 504 6 HET GOL A 505 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 SO4 O4 S 2- FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *669(H2 O) HELIX 1 AA1 SER A 4 THR A 8 5 5 HELIX 2 AA2 GLY A 17 SER A 30 1 14 HELIX 3 AA3 THR A 33 SER A 35 5 3 HELIX 4 AA4 ASP A 64 ASP A 77 1 14 HELIX 5 AA5 PHE A 80 LYS A 82 5 3 HELIX 6 AA6 GLY A 95 ASP A 111 1 17 HELIX 7 AA7 SER A 123 MET A 131 1 9 HELIX 8 AA8 THR A 135 ILE A 139 5 5 HELIX 9 AA9 ALA A 154 GLY A 170 1 17 HELIX 10 AB1 GLY A 177 GLY A 179 5 3 HELIX 11 AB2 ALA A 211 ALA A 213 5 3 HELIX 12 AB3 TRP A 214 VAL A 219 1 6 HELIX 13 AB4 THR A 238 ARG A 244 1 7 HELIX 14 AB5 PRO A 309 MET A 324 1 16 HELIX 15 AB6 PRO A 325 LYS A 328 5 4 HELIX 16 AB7 SER A 369 LEU A 373 5 5 HELIX 17 AB8 ILE A 375 GLU A 385 1 11 HELIX 18 AB9 ALA A 389 TRP A 396 1 8 HELIX 19 AC1 ALA A 418 MET A 420 5 3 SHEET 1 AA1 6 ARG A 172 PHE A 175 0 SHEET 2 AA1 6 VAL A 37 ASP A 41 1 N VAL A 39 O ARG A 172 SHEET 3 AA1 6 VAL A 10 VAL A 13 1 N VAL A 12 O THR A 38 SHEET 4 AA1 6 LYS A 206 LEU A 209 1 O VAL A 208 N VAL A 13 SHEET 5 AA1 6 PHE A 359 THR A 363 1 O TYR A 360 N LEU A 209 SHEET 6 AA1 6 LEU A 349 GLU A 352 -1 N CYS A 351 O LEU A 361 SHEET 1 AA2 3 LYS A 57 MET A 59 0 SHEET 2 AA2 3 GLY A 151 LEU A 153 -1 O LEU A 153 N LYS A 57 SHEET 3 AA2 3 PHE A 84 HIS A 85 -1 N HIS A 85 O TRP A 152 SHEET 1 AA3 8 VAL A 118 LEU A 121 0 SHEET 2 AA3 8 LYS A 143 SER A 147 -1 O ALA A 144 N LEU A 121 SHEET 3 AA3 8 ARG A 89 ALA A 93 -1 N ASP A 91 O ILE A 145 SHEET 4 AA3 8 VAL A 250 ASN A 253 1 O VAL A 250 N LEU A 90 SHEET 5 AA3 8 GLY A 257 PHE A 259 -1 N GLY A 257 O ASN A 253 SHEET 6 AA3 8 ILE A 267 CYS A 271 -1 O CYS A 271 N PHE A 258 SHEET 7 AA3 8 CYS A 225 GLN A 236 -1 N GLY A 233 O VAL A 270 SHEET 8 AA3 8 PHE A 333 THR A 343 -1 O CYS A 340 N LYS A 228 SHEET 1 AA4 3 PHE A 181 ALA A 187 0 SHEET 2 AA4 3 VAL A 190 THR A 196 -1 O ILE A 192 N LEU A 185 SHEET 3 AA4 3 ARG A 201 TYR A 203 -1 O TYR A 202 N VAL A 194 SHEET 1 AA5 2 PHE A 277 THR A 278 0 SHEET 2 AA5 2 LYS A 415 ASP A 416 1 O LYS A 415 N THR A 278 SHEET 1 AA6 2 PHE A 280 HIS A 283 0 SHEET 2 AA6 2 LYS A 292 SER A 295 -1 O LYS A 292 N HIS A 283 LINK SG CYS A 338 C8M FAD A 501 1555 1555 1.87 CISPEP 1 ILE A 45 PRO A 46 0 -14.33 SITE 1 AC1 37 VAL A 13 GLY A 14 GLY A 16 GLY A 17 SITE 2 AC1 37 THR A 18 ILE A 19 ASP A 41 ALA A 42 SITE 3 AC1 37 SER A 47 GLN A 49 SER A 50 ALA A 51 SITE 4 AC1 37 LYS A 57 ILE A 58 GLY A 179 SER A 180 SITE 5 AC1 37 PHE A 181 ALA A 210 ALA A 211 GLY A 212 SITE 6 AC1 37 TRP A 214 LEU A 218 CYS A 338 CYS A 340 SITE 7 AC1 37 ASP A 365 GLY A 367 ASP A 368 SER A 369 SITE 8 AC1 37 PHE A 370 LYS A 371 GOL A 503 HOH A 655 SITE 9 AC1 37 HOH A 695 HOH A 713 HOH A 749 HOH A 763 SITE 10 AC1 37 HOH A 931 SITE 1 AC2 7 ARG A 279 ARG A 298 HIS A 303 HOH A 726 SITE 2 AC2 7 HOH A 907 HOH A 923 HOH A 929 SITE 1 AC3 8 TRP A 230 GLY A 367 ARG A 410 FAD A 501 SITE 2 AC3 8 HOH A 611 HOH A 751 HOH A 899 HOH A 995 SITE 1 AC4 5 ARG A 89 ASP A 91 TYR A 252 HOH A 710 SITE 2 AC4 5 HOH A 928 SITE 1 AC5 8 HIS A 234 ILE A 267 ASN A 334 HOH A 606 SITE 2 AC5 8 HOH A 643 HOH A 744 HOH A 885 HOH A1143 CRYST1 90.033 90.033 131.435 90.00 90.00 90.00 P 42 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 0.011107 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007608 0.00000