HEADER OXIDOREDUCTASE 20-DEC-16 5MQ6 TITLE POLYCYCLIC KETONE MONOOXYGENASE FROM THE THERMOPHILIC FUNGUS TITLE 2 THERMOTHELOMYCES THERMOPHILA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCELIOPHTHORA THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 78579; SOURCE 4 ATCC: 42464; SOURCE 5 GENE: MYCTH_65400; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-HIS6-SUMO KEYWDS FLAVIN, MONOOXYGENASE, BAEYER-VILLIGER, OXYGEN, BIOCATALYSIS, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SAVINO,M.J.L.J.FURST,M.W.FRAAIJE,A.MATTEVI REVDAT 4 17-JAN-24 5MQ6 1 REMARK REVDAT 3 22-APR-20 5MQ6 1 REMARK REVDAT 2 25-JAN-17 5MQ6 1 JRNL REVDAT 1 11-JAN-17 5MQ6 0 JRNL AUTH M.J.FURST,S.SAVINO,H.M.DUDEK,J.R.GOMEZ CASTELLANOS, JRNL AUTH 2 C.GUTIERREZ DE SOUZA,S.ROVIDA,M.W.FRAAIJE,A.MATTEVI JRNL TITL POLYCYCLIC KETONE MONOOXYGENASE FROM THE THERMOPHILIC FUNGUS JRNL TITL 2 THERMOTHELOMYCES THERMOPHILA: A STRUCTURALLY DISTINCT JRNL TITL 3 BIOCATALYST FOR BULKY SUBSTRATES. JRNL REF J. AM. CHEM. SOC. V. 139 627 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28010060 JRNL DOI 10.1021/JACS.6B12246 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 48005 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1541 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3519 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4965 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 365 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : 0.95000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.993 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5204 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4835 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7083 ; 2.129 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11148 ; 2.106 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 636 ; 7.058 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;35.030 ;23.553 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 833 ;16.779 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.712 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 753 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5841 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1190 ; 0.010 ; 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): 2544 ; 4.572 ; 3.025 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2543 ; 4.558 ; 3.025 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3177 ; 5.258 ; 4.521 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3178 ; 5.260 ; 4.521 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2660 ; 4.753 ; 3.392 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2660 ; 4.753 ; 3.392 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3906 ; 5.224 ; 4.923 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6515 ; 5.794 ;36.750 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6367 ; 5.724 ;36.409 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 10039 ; 6.759 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 113 ;24.613 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 10155 ;10.267 ; 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 : 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 REMARK 4 REMARK 4 5MQ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-13 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 75.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.16200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 1.20700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 2YLT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.7 M AMMONIUM SULFATE, 100 MM MES REMARK 280 SODIUM SALT PH 6.5, AND 5% V/V PEG400, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K 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 29.60000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.76000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.76000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.60000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.51000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 ALA A 2 REMARK 465 PRO A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 ALA A 11 REMARK 465 PRO A 12 REMARK 465 THR A 13 REMARK 465 LEU A 608 REMARK 465 ARG A 609 REMARK 465 LYS A 610 REMARK 465 SER A 611 REMARK 465 GLU A 612 REMARK 465 ASP A 613 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 1128 O HOH A 1140 1.75 REMARK 500 O HOH A 1160 O HOH A 1165 1.89 REMARK 500 NH1 ARG A 193 O ARG A 654 1.93 REMARK 500 SG CYS A 132 O4 FAD A 700 1.96 REMARK 500 O HOH A 1069 O HOH A 1161 2.01 REMARK 500 O VAL A 563 O HOH A 801 2.01 REMARK 500 O HOH A 801 O HOH A 848 2.06 REMARK 500 O HOH A 801 O HOH A 912 2.07 REMARK 500 O HOH A 801 O HOH A 1011 2.11 REMARK 500 O HOH A 1108 O HOH A 1125 2.11 REMARK 500 O HOH A 846 O HOH A 1137 2.12 REMARK 500 O PRO A 378 O HOH A 802 2.19 REMARK 500 OE2 GLU A 397 O HOH A 803 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 75 O HOH A 801 4465 1.96 REMARK 500 O HOH A 801 O HOH A 914 4565 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 SER A 338 CB SER A 338 OG 0.079 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 33 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 CYS A 132 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 203 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 253 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 300 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 324 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 332 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 332 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 400 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 400 NE - CZ - NH1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG A 400 NE - CZ - NH2 ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG A 402 CD - NE - CZ ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 402 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 402 NE - CZ - NH2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ASP A 643 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 643 CB - CG - OD2 ANGL. DEV. = -7.5 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 20 44.72 -78.02 REMARK 500 ALA A 103 57.78 -140.53 REMARK 500 ARG A 126 31.40 -140.92 REMARK 500 GLU A 135 129.33 -39.02 REMARK 500 ILE A 322 -74.78 -117.64 REMARK 500 ASP A 354 -168.16 -122.73 REMARK 500 PRO A 376 44.50 -88.78 REMARK 500 ALA A 463 53.28 38.64 REMARK 500 ASP A 464 -5.32 62.61 REMARK 500 SER A 475 53.90 -115.27 REMARK 500 LEU A 532 -85.02 -122.84 REMARK 500 SER A 535 -129.87 -142.54 REMARK 500 ASP A 566 68.01 77.35 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 HIS A 20 GLN A 21 141.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NDP A 701 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 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NDP A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 702 DBREF 5MQ6 A 1 655 UNP G2QA95 G2QA95_MYCTT 1 655 SEQRES 1 A 655 MET ALA PRO SER ALA GLU GLY ALA SER GLY ALA PRO THR SEQRES 2 A 655 PRO GLU ASP LEU LYS LEU HIS GLN LEU SER GLN LYS TYR SEQRES 3 A 655 THR ALA GLU ALA ALA LYS ARG PHE ARG PRO GLU GLY LEU SEQRES 4 A 655 GLY GLN PHE ILE ARG LEU LYS GLU VAL GLY ASN GLU ARG SEQRES 5 A 655 PHE ARG ALA LEU ALA GLU ASP PRO TRP VAL ASP HIS ALA SEQRES 6 A 655 ALA LEU ASN ALA LYS GLU PRO VAL LYS ASP GLY SER ARG SEQRES 7 A 655 TYR LYS PHE ILE ILE LEU GLY ALA GLY TYR GLY GLY LEU SEQRES 8 A 655 LEU TYR ALA VAL ARG LEU ALA GLU ALA GLY LEU ALA SER SEQRES 9 A 655 GLY PRO ASP ASP ILE LEU MET VAL ASP ALA ALA GLY GLY SEQRES 10 A 655 PHE GLY GLY THR TRP TRP TRP ASN ARG TYR PRO GLY LEU SEQRES 11 A 655 HIS CYS ASP VAL GLU SER TYR SER TYR MET PRO LEU LEU SEQRES 12 A 655 GLU GLU THR GLY TYR ILE PRO LYS SER LYS TYR ALA ALA SEQRES 13 A 655 GLY PRO GLU LEU LEU GLU HIS ALA TYR ARG ILE ALA THR SEQRES 14 A 655 GLN TRP LYS LEU HIS ASP LYS ALA LEU PHE ARG SER ASN SEQRES 15 A 655 VAL LYS THR ILE ARG TRP ASP ASP GLU SER ARG LEU TRP SEQRES 16 A 655 SER LEU GLU VAL THR GLU GLY ARG GLY PRO GLY GLN GLN SEQRES 17 A 655 SER ARG GLU LEU LYS LEU GLN ALA ARG TYR VAL LEU LEU SEQRES 18 A 655 ALA SER GLY ILE LEU THR ASN PRO GLN VAL PRO LYS ILE SEQRES 19 A 655 PRO GLY LEU GLU THR PHE THR GLY PRO VAL PHE HIS THR SEQRES 20 A 655 ALA ARG TRP ASN TYR ASP VAL THR GLY GLY SER PRO THR SEQRES 21 A 655 ASP GLU ALA LEU ASN ARG LEU GLU GLY LYS ARG VAL GLY SEQRES 22 A 655 ILE ILE GLY THR GLY ALA THR ALA ILE GLN VAL VAL PRO SEQRES 23 A 655 LYS LEU ALA LYS TYR ALA LYS GLU LEU TYR VAL PHE GLN SEQRES 24 A 655 ARG THR PRO SER GLY VAL TRP TRP ARG GLY GLN ARG PRO SEQRES 25 A 655 THR ASP PRO VAL GLU TRP LYS THR LYS ILE ALA ARG LYS SEQRES 26 A 655 LYS GLY TRP GLN ARG GLU ARG MET LEU ASN LEU ASP SER SEQRES 27 A 655 TYR LEU THR ASP ALA ALA GLU GLU GLY GLN GLU ASN MET SEQRES 28 A 655 VAL ALA ASP GLY TRP THR GLU MET PRO ALA PHE SER ALA SEQRES 29 A 655 VAL ILE GLY SER PRO ARG HIS GLY ILE VAL GLU PRO THR SEQRES 30 A 655 PRO GLU LYS ILE ALA GLU HIS LEU GLY ARG LEU TYR LYS SEQRES 31 A 655 LEU ASP LEU PRO HIS ALA GLU GLN VAL ARG ALA ARG THR SEQRES 32 A 655 ASP SER ILE VAL LYS ASP PRO LYS THR ALA ALA LYS LEU SEQRES 33 A 655 LYS ALA TRP TYR PRO THR TRP CYS LYS ARG PRO THR PHE SEQRES 34 A 655 SER ASP GLU TYR LEU GLN THR PHE ASN LEU PRO ASN VAL SEQRES 35 A 655 HIS LEU VAL ASP THR ASP GLY LYS GLY VAL ASP ALA ALA SEQRES 36 A 655 ASN PRO SER GLY LEU VAL VAL ALA ASP LYS GLU TYR PRO SEQRES 37 A 655 LEU ASP ILE LEU VAL LEU SER THR GLY TYR VAL THR PRO SEQRES 38 A 655 SER ILE GLY GLY GLY SER PRO ALA VAL ARG THR GLY VAL SEQRES 39 A 655 ASP ILE TYR GLY ARG GLY GLY LYS SER LEU ASP ASP LYS SEQRES 40 A 655 TRP GLN THR HIS GLY ALA ALA THR LEU HIS GLY VAL CYS SEQRES 41 A 655 SER ASN GLY PHE PRO ASN LEU PHE PHE THR PRO LEU SER SEQRES 42 A 655 GLN SER SER GLN ALA ALA ASN ASN ALA PHE THR LEU ASP SEQRES 43 A 655 VAL GLY THR GLU HIS ILE VAL GLN VAL ILE LYS THR ALA SEQRES 44 A 655 GLU ASP ARG VAL ASP GLY ASP ALA LEU VAL GLU VAL THR SEQRES 45 A 655 SER GLU ALA GLU GLU ALA TRP SER PHE GLU ILE MET LYS SEQRES 46 A 655 HIS ALA GLY TRP PHE ALA SER VAL THR GLY CYS THR PRO SEQRES 47 A 655 GLY TYR ILE THR SER GLU GLY GLU ALA LEU ARG LYS SER SEQRES 48 A 655 GLU ASP PRO MET GLU MET ALA LYS ARG ALA ARG SER GLY SEQRES 49 A 655 ASN LEU SER GLN GLY MET ALA SER TYR MET LYS LEU LEU SEQRES 50 A 655 GLN GLU TYR ARG ALA ASP GLY SER LEU LYS GLY PHE ASP SEQRES 51 A 655 ILE SER SER ARG ALA HET FAD A 700 53 HET NDP A 701 39 HET GOL A 702 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 NDP C21 H30 N7 O17 P3 FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *365(H2 O) HELIX 1 AA1 PRO A 14 HIS A 20 1 7 HELIX 2 AA2 GLN A 21 LYS A 32 1 12 HELIX 3 AA3 GLU A 37 GLY A 40 5 4 HELIX 4 AA4 LYS A 46 VAL A 48 5 3 HELIX 5 AA5 ASN A 50 ALA A 55 1 6 HELIX 6 AA6 LEU A 56 GLU A 58 5 3 HELIX 7 AA7 ASP A 63 ALA A 69 1 7 HELIX 8 AA8 GLY A 87 ALA A 100 1 14 HELIX 9 AA9 GLY A 120 ASN A 125 1 6 HELIX 10 AB1 GLU A 135 MET A 140 1 6 HELIX 11 AB2 LEU A 142 GLY A 147 1 6 HELIX 12 AB3 ALA A 156 TRP A 171 1 16 HELIX 13 AB4 GLY A 236 PHE A 240 5 5 HELIX 14 AB5 ALA A 248 TRP A 250 5 3 HELIX 15 AB6 ASN A 251 GLY A 256 1 6 HELIX 16 AB7 LEU A 264 GLU A 268 5 5 HELIX 17 AB8 GLY A 278 LYS A 290 1 13 HELIX 18 AB9 ASP A 314 ILE A 322 1 9 HELIX 19 AC1 GLY A 327 THR A 341 1 15 HELIX 20 AC2 ASP A 354 ALA A 361 5 8 HELIX 21 AC3 PHE A 362 GLY A 367 1 6 HELIX 22 AC4 THR A 377 VAL A 407 1 31 HELIX 23 AC5 ASP A 409 LYS A 417 1 9 HELIX 24 AC6 PRO A 421 LYS A 425 5 5 HELIX 25 AC7 GLU A 432 PHE A 437 1 6 HELIX 26 AC8 SER A 482 GLY A 486 5 5 HELIX 27 AC9 SER A 487 GLY A 493 1 7 HELIX 28 AD1 GLY A 498 LYS A 502 5 5 HELIX 29 AD2 SER A 503 GLY A 512 1 10 HELIX 30 AD3 ASN A 540 VAL A 563 1 24 HELIX 31 AD4 THR A 572 HIS A 586 1 15 HELIX 32 AD5 ALA A 587 THR A 594 5 8 HELIX 33 AD6 GLY A 599 SER A 603 5 5 HELIX 34 AD7 MET A 615 ARG A 622 1 8 HELIX 35 AD8 GLY A 629 ALA A 642 1 14 SHEET 1 AA1 2 PHE A 42 ARG A 44 0 SHEET 2 AA1 2 GLN A 230 PRO A 232 -1 O VAL A 231 N ILE A 43 SHEET 1 AA2 7 ALA A 177 LEU A 178 0 SHEET 2 AA2 7 ILE A 109 VAL A 112 1 N MET A 111 O LEU A 178 SHEET 3 AA2 7 ARG A 78 LEU A 84 1 N ILE A 83 O VAL A 112 SHEET 4 AA2 7 ARG A 210 LEU A 221 1 O LEU A 220 N ILE A 82 SHEET 5 AA2 7 LEU A 194 GLU A 201 -1 N VAL A 199 O LEU A 212 SHEET 6 AA2 7 SER A 181 ASP A 189 -1 N LYS A 184 O GLU A 198 SHEET 7 AA2 7 ASP A 495 TYR A 497 1 O TYR A 497 N ILE A 186 SHEET 1 AA3 5 ALA A 177 LEU A 178 0 SHEET 2 AA3 5 ILE A 109 VAL A 112 1 N MET A 111 O LEU A 178 SHEET 3 AA3 5 ARG A 78 LEU A 84 1 N ILE A 83 O VAL A 112 SHEET 4 AA3 5 ARG A 210 LEU A 221 1 O LEU A 220 N ILE A 82 SHEET 5 AA3 5 LEU A 527 PHE A 529 1 O PHE A 528 N LEU A 221 SHEET 1 AA4 5 VAL A 244 HIS A 246 0 SHEET 2 AA4 5 ILE A 471 LEU A 474 1 O LEU A 474 N PHE A 245 SHEET 3 AA4 5 ARG A 271 ILE A 275 1 N GLY A 273 O VAL A 473 SHEET 4 AA4 5 GLU A 294 GLN A 299 1 O PHE A 298 N ILE A 274 SHEET 5 AA4 5 VAL A 442 ASP A 446 1 O VAL A 445 N VAL A 297 SHEET 1 AA5 2 VAL A 305 TRP A 306 0 SHEET 2 AA5 2 THR A 428 PHE A 429 1 O THR A 428 N TRP A 306 SHEET 1 AA6 3 ALA A 454 ASN A 456 0 SHEET 2 AA6 3 GLY A 459 VAL A 462 -1 O GLY A 459 N ASN A 456 SHEET 3 AA6 3 LYS A 465 PRO A 468 -1 O TYR A 467 N LEU A 460 SHEET 1 AA7 2 ALA A 567 VAL A 571 0 SHEET 2 AA7 2 PHE A 649 SER A 653 -1 O ASP A 650 N GLU A 570 SSBOND 1 CYS A 424 CYS A 596 1555 1555 2.10 SITE 1 AC1 36 LEU A 84 GLY A 85 GLY A 87 TYR A 88 SITE 2 AC1 36 GLY A 89 ASP A 113 ALA A 114 GLY A 120 SITE 3 AC1 36 THR A 121 TRP A 124 CYS A 132 ASP A 133 SITE 4 AC1 36 VAL A 134 TYR A 139 SER A 181 ASN A 182 SITE 5 AC1 36 VAL A 183 ALA A 222 SER A 223 GLY A 224 SITE 6 AC1 36 THR A 227 ARG A 426 TYR A 478 THR A 492 SITE 7 AC1 36 VAL A 494 ALA A 539 ASN A 540 ASN A 541 SITE 8 AC1 36 NDP A 701 HOH A 804 HOH A 860 HOH A 886 SITE 9 AC1 36 HOH A 905 HOH A 936 HOH A1030 HOH A1036 SITE 1 AC2 29 PHE A 42 PRO A 232 ILE A 275 GLY A 276 SITE 2 AC2 29 THR A 277 GLY A 278 ALA A 279 THR A 280 SITE 3 AC2 29 ARG A 300 THR A 301 LYS A 425 ARG A 426 SITE 4 AC2 29 GLY A 451 VAL A 452 SER A 475 THR A 476 SITE 5 AC2 29 GLY A 477 TYR A 478 TYR A 600 FAD A 700 SITE 6 AC2 29 HOH A 833 HOH A 843 HOH A 877 HOH A 879 SITE 7 AC2 29 HOH A 884 HOH A 899 HOH A 902 HOH A 948 SITE 8 AC2 29 HOH A 980 SITE 1 AC3 8 ALA A 396 VAL A 399 ARG A 400 ALA A 418 SITE 2 AC3 8 TYR A 420 THR A 422 HOH A 827 HOH A 845 CRYST1 59.200 91.020 133.520 90.00 90.00 90.00 P 21 21 21 4 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 0.016892 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010987 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007490 0.00000