HEADER HYDROLASE 15-APR-16 5JCI TITLE STRUCTURE AND CATALYTIC MECHANISM OF MONODEHYDROASCORBATE REDUCTASE, TITLE 2 MDHAR, FROM ORYZA SATIVA L. JAPONICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: OS09G0567300 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 4-435; COMPND 5 SYNONYM: PUTATIVE MONODEHYDROASCORBATE REDUCTASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. JAPONICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: OS09G0567300, OS09G0567300, OJ1155_H10.27, OSNPB_090567300; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.PARK,H.W.KIM REVDAT 2 20-MAR-24 5JCI 1 REMARK REVDAT 1 12-OCT-16 5JCI 0 JRNL AUTH A.K.PARK,I.S.KIM,H.DO,B.W.JEON,C.W.LEE,S.J.ROH,S.C.SHIN, JRNL AUTH 2 H.PARK,Y.S.KIM,Y.H.KIM,H.S.YOON,J.H.LEE,H.W.KIM JRNL TITL STRUCTURE AND CATALYTIC MECHANISM OF MONODEHYDROASCORBATE JRNL TITL 2 REDUCTASE, MDHAR, FROM ORYZA SATIVA L. JAPONICA JRNL REF SCI REP V. 6 33903 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27652777 JRNL DOI 10.1038/SREP33903 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 42704 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2140 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3108 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.2260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3278 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 481 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.03000 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): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.759 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3406 ; 0.030 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3247 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4619 ; 2.657 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7499 ; 1.246 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 6.005 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;35.680 ;24.741 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 557 ;15.193 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;12.867 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 509 ; 0.183 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3830 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 734 ; 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): 1727 ; 2.400 ; 1.914 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1726 ; 2.393 ; 1.912 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2157 ; 3.193 ; 2.867 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 : 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 5JCI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220360. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97954 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85440 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 67.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, LITHIUM SULFATE, PEG 5000 MME, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 60.33250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.63500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.16625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.63500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.63500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.49875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.63500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.16625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.63500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.49875 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 60.33250 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: 1430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 740 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 837 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 -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 ALA A -11 REMARK 465 SER A -10 REMARK 465 GLU A -9 REMARK 465 ASN A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 PHE A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 VAL A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 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 830 O HOH A 988 1.77 REMARK 500 O HOH A 832 O HOH A 989 1.91 REMARK 500 O HOH A 1024 O HOH A 1036 2.01 REMARK 500 NH1 ARG A 351 O HOH A 601 2.07 REMARK 500 O HOH A 798 O HOH A 940 2.10 REMARK 500 O HOH A 818 O HOH A 1036 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 O HOH A 647 O HOH A 1015 7555 2.11 REMARK 500 O HOH A 800 O HOH A 1040 4454 2.11 REMARK 500 O HOH A 603 O HOH A 929 7455 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 GLU A 4 CG GLU A 4 CD 0.092 REMARK 500 GLU A 4 CD GLU A 4 OE2 0.068 REMARK 500 GLU A 47 CD GLU A 47 OE1 0.067 REMARK 500 ARG A 63 CZ ARG A 63 NH1 -0.079 REMARK 500 GLU A 76 CD GLU A 76 OE2 0.078 REMARK 500 GLU A 117 CD GLU A 117 OE2 0.081 REMARK 500 ASP A 139 CB ASP A 139 CG 0.216 REMARK 500 ASP A 139 CG ASP A 139 OD1 0.144 REMARK 500 ASP A 139 CG ASP A 139 OD2 0.160 REMARK 500 TYR A 174 CE1 TYR A 174 CZ 0.103 REMARK 500 GLU A 314 CD GLU A 314 OE2 0.078 REMARK 500 TYR A 347 CE1 TYR A 347 CZ -0.104 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 23 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 LYS A 31 CD - CE - NZ ANGL. DEV. = 17.5 DEGREES REMARK 500 PHE A 57 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 LEU A 78 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 GLU A 117 OE1 - CD - OE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP A 139 CB - CG - OD1 ANGL. DEV. = 8.9 DEGREES REMARK 500 ASP A 187 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 TYR A 216 CD1 - CE1 - CZ ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 235 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 263 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 298 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 298 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 312 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 312 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 317 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 VAL A 340 CG1 - CB - CG2 ANGL. DEV. = 13.4 DEGREES REMARK 500 ARG A 351 NH1 - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 351 NE - CZ - NH1 ANGL. DEV. = -7.3 DEGREES REMARK 500 TYR A 360 CD1 - CE1 - CZ ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 403 CB - CG - OD2 ANGL. DEV. = -7.1 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 LYS A 53 -103.55 -126.01 REMARK 500 ARG A 147 -45.16 -131.51 REMARK 500 ASP A 187 38.68 72.66 REMARK 500 LEU A 203 -51.78 -126.28 REMARK 500 GLU A 314 64.51 -113.05 REMARK 500 PHE A 353 -139.86 44.11 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 A1081 DISTANCE = 5.92 ANGSTROMS 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 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JCN RELATED DB: PDB REMARK 900 RELATED ID: 5JCM RELATED DB: PDB REMARK 900 RELATED ID: 5JCL RELATED DB: PDB REMARK 900 RELATED ID: 5JCK RELATED DB: PDB DBREF 5JCI A 4 435 UNP Q652L6 Q652L6_ORYSJ 4 435 SEQADV 5JCI HIS A -17 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI HIS A -16 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI HIS A -15 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI HIS A -14 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI HIS A -13 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI HIS A -12 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI ALA A -11 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI SER A -10 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI GLU A -9 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI ASN A -8 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI LEU A -7 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI TYR A -6 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI PHE A -5 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI GLN A -4 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI GLY A -3 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI ALA A -2 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI MET A -1 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI VAL A 0 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI MET A 1 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI ALA A 2 UNP Q652L6 EXPRESSION TAG SEQADV 5JCI SER A 3 UNP Q652L6 EXPRESSION TAG SEQRES 1 A 453 HIS HIS HIS HIS HIS HIS ALA SER GLU ASN LEU TYR PHE SEQRES 2 A 453 GLN GLY ALA MET VAL MET ALA SER GLU LYS HIS PHE LYS SEQRES 3 A 453 TYR VAL ILE LEU GLY GLY GLY VAL ALA ALA GLY TYR ALA SEQRES 4 A 453 ALA ARG GLU PHE ALA LYS GLN GLY VAL LYS PRO GLY GLU SEQRES 5 A 453 LEU ALA ILE ILE SER LYS GLU ALA VAL ALA PRO TYR GLU SEQRES 6 A 453 ARG PRO ALA LEU SER LYS GLY TYR LEU PHE PRO GLN ASN SEQRES 7 A 453 ALA ALA ARG LEU PRO GLY PHE HIS VAL CYS VAL GLY SER SEQRES 8 A 453 GLY GLY GLU ARG LEU LEU PRO GLU TRP TYR SER GLU LYS SEQRES 9 A 453 GLY ILE GLU LEU ILE LEU SER THR GLU ILE VAL LYS ALA SEQRES 10 A 453 ASP LEU ALA SER LYS THR LEU THR SER ALA VAL GLY ALA SEQRES 11 A 453 THR PHE THR TYR GLU ILE LEU ILE ILE ALA THR GLY SER SEQRES 12 A 453 SER VAL ILE LYS LEU SER ASP PHE GLY THR GLN GLY ALA SEQRES 13 A 453 ASP SER ASN ASN ILE LEU TYR LEU ARG GLU VAL ASP ASP SEQRES 14 A 453 ALA ASP LYS LEU VAL ALA ALA ILE GLN ALA LYS LYS GLY SEQRES 15 A 453 GLY LYS ALA VAL ILE VAL GLY GLY GLY TYR ILE GLY LEU SEQRES 16 A 453 GLU LEU SER ALA ALA LEU LYS ILE ASN ASP PHE ASP VAL SEQRES 17 A 453 THR MET VAL PHE PRO GLU PRO TRP CYS MET PRO ARG LEU SEQRES 18 A 453 PHE THR ALA ASP ILE ALA ALA PHE TYR GLU SER TYR TYR SEQRES 19 A 453 THR ASN LYS GLY VAL LYS ILE VAL LYS GLY THR VAL ALA SEQRES 20 A 453 VAL GLY PHE ASP ALA ASP ALA ASN GLY ASP VAL THR ALA SEQRES 21 A 453 VAL ASN LEU LYS ASN GLY SER VAL LEU GLU ALA ASP ILE SEQRES 22 A 453 VAL VAL VAL GLY VAL GLY GLY ARG PRO LEU THR THR LEU SEQRES 23 A 453 PHE LYS GLY GLN VAL ALA GLU GLU LYS GLY GLY ILE LYS SEQRES 24 A 453 THR ASP ALA PHE PHE GLU THR SER VAL PRO GLY VAL TYR SEQRES 25 A 453 ALA VAL GLY ASP VAL ALA THR PHE PRO MET LYS MET TYR SEQRES 26 A 453 ASN GLU LEU ARG ARG VAL GLU HIS VAL ASP HIS ALA ARG SEQRES 27 A 453 LYS SER ALA GLU GLN ALA VAL LYS ALA ILE LYS GLY LYS SEQRES 28 A 453 GLU SER GLY GLU SER VAL VAL GLU TYR ASP TYR LEU PRO SEQRES 29 A 453 TYR PHE TYR SER ARG SER PHE ASP LEU GLY TRP GLN PHE SEQRES 30 A 453 TYR GLY ASP ASN VAL GLY ASP THR ILE LEU PHE GLY ASP SEQRES 31 A 453 SER ASP PRO THR SER ALA LYS PRO LYS PHE GLY SER TYR SEQRES 32 A 453 TRP ILE LYS ASP GLY LYS VAL LEU GLY ALA PHE LEU GLU SEQRES 33 A 453 GLY GLY SER PRO ASP GLU ASN LYS ALA ILE ALA LYS VAL SEQRES 34 A 453 ALA LYS THR GLN PRO PRO VAL ALA ASN ILE GLU GLU LEU SEQRES 35 A 453 LYS LYS GLU GLY LEU GLN PHE ALA SER LYS ILE HET FAD A 500 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *481(H2 O) HELIX 1 AA1 GLY A 15 GLN A 28 1 14 HELIX 2 AA2 GLU A 47 PHE A 57 5 11 HELIX 3 AA3 CYS A 70 GLY A 74 5 5 HELIX 4 AA4 LEU A 79 LYS A 86 1 8 HELIX 5 AA5 LYS A 129 GLY A 134 5 6 HELIX 6 AA6 GLU A 148 LYS A 162 1 15 HELIX 7 AA7 GLY A 173 ASN A 186 1 14 HELIX 8 AA8 THR A 205 LYS A 219 1 15 HELIX 9 AA9 THR A 266 LYS A 270 5 5 HELIX 10 AB1 LYS A 305 ASN A 308 5 4 HELIX 11 AB2 HIS A 315 GLY A 336 1 22 HELIX 12 AB3 SER A 401 GLN A 415 1 15 HELIX 13 AB4 ASN A 420 GLU A 427 1 8 HELIX 14 AB5 GLU A 427 ILE A 435 1 9 SHEET 1 AA1 6 GLU A 89 ILE A 91 0 SHEET 2 AA1 6 LEU A 35 ILE A 38 1 N ILE A 37 O ILE A 91 SHEET 3 AA1 6 LYS A 5 LEU A 12 1 N ILE A 11 O ALA A 36 SHEET 4 AA1 6 THR A 113 ILE A 121 1 O ILE A 120 N LEU A 12 SHEET 5 AA1 6 THR A 105 SER A 108 -1 N LEU A 106 O PHE A 114 SHEET 6 AA1 6 ILE A 96 ASP A 100 -1 N VAL A 97 O THR A 107 SHEET 1 AA2 5 GLU A 89 ILE A 91 0 SHEET 2 AA2 5 LEU A 35 ILE A 38 1 N ILE A 37 O ILE A 91 SHEET 3 AA2 5 LYS A 5 LEU A 12 1 N ILE A 11 O ALA A 36 SHEET 4 AA2 5 THR A 113 ILE A 121 1 O ILE A 120 N LEU A 12 SHEET 5 AA2 5 VAL A 293 ALA A 295 1 O TYR A 294 N LEU A 119 SHEET 1 AA3 2 SER A 125 VAL A 127 0 SHEET 2 AA3 2 GLY A 262 PRO A 264 -1 O ARG A 263 N SER A 126 SHEET 1 AA4 5 ILE A 143 TYR A 145 0 SHEET 2 AA4 5 ILE A 255 VAL A 258 1 O VAL A 256 N LEU A 144 SHEET 3 AA4 5 LYS A 166 VAL A 170 1 N VAL A 168 O VAL A 257 SHEET 4 AA4 5 ASP A 189 PHE A 194 1 O ASP A 189 N ALA A 167 SHEET 5 AA4 5 LYS A 222 LYS A 225 1 O VAL A 224 N MET A 192 SHEET 1 AA5 3 ALA A 229 ALA A 234 0 SHEET 2 AA5 3 VAL A 240 LEU A 245 -1 O ASN A 244 N VAL A 230 SHEET 3 AA5 3 VAL A 250 GLU A 252 -1 O LEU A 251 N VAL A 243 SHEET 1 AA6 4 GLU A 275 GLU A 276 0 SHEET 2 AA6 4 GLY A 279 LYS A 281 -1 O GLY A 279 N GLU A 276 SHEET 3 AA6 4 ALA A 300 MET A 304 1 O THR A 301 N ILE A 280 SHEET 4 AA6 4 GLU A 309 ARG A 311 -1 O GLU A 309 N MET A 304 SHEET 1 AA7 5 TYR A 347 SER A 352 0 SHEET 2 AA7 5 LEU A 355 GLY A 361 -1 O PHE A 359 N PHE A 348 SHEET 3 AA7 5 LYS A 391 GLU A 398 -1 O ALA A 395 N TYR A 360 SHEET 4 AA7 5 LYS A 381 LYS A 388 -1 N PHE A 382 O GLU A 398 SHEET 5 AA7 5 ASP A 366 ASP A 372 -1 N ASP A 366 O ILE A 387 CISPEP 1 LEU A 64 PRO A 65 0 6.54 CISPEP 2 VAL A 69 CYS A 70 0 -2.39 SITE 1 AC1 35 GLY A 13 GLY A 14 GLY A 15 VAL A 16 SITE 2 AC1 35 ALA A 17 SER A 39 LYS A 40 GLU A 41 SITE 3 AC1 35 ARG A 48 PRO A 49 SER A 52 LYS A 53 SITE 4 AC1 35 THR A 94 GLU A 95 ILE A 96 ALA A 122 SITE 5 AC1 35 THR A 123 GLY A 124 ARG A 147 GLU A 148 SITE 6 AC1 35 TYR A 174 ILE A 175 GLY A 297 ASP A 298 SITE 7 AC1 35 GLU A 314 HIS A 315 VAL A 316 ALA A 319 SITE 8 AC1 35 PHE A 348 TYR A 349 HOH A 677 HOH A 683 SITE 9 AC1 35 HOH A 710 HOH A 738 HOH A 881 CRYST1 81.270 81.270 120.665 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 0.012305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008287 0.00000