HEADER OXIDOREDUCTASE 05-JUL-18 6H00 TITLE CRYSTAL STRUCTURE OF HUMAN PYRIDOXINE 5-PHOPHATE OXIDASE, R116Q TITLE 2 VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXINE-5'-PHOSPHATE OXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRIDOXAMINE-PHOSPHATE OXIDASE; COMPND 5 EC: 1.4.3.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PNPO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PNPO, FMN-BINDING, PNP-OXIDASE ACTIVITY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MACKINNON,M.P.WILSON,L.SHRESTHA,G.A.BEZERRA,J.NEWMAN,N.FOX, AUTHOR 2 F.SORRELL,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,P.T.CLAYTON,P.B.MILLS, AUTHOR 3 W.W.YUE REVDAT 2 17-JAN-24 6H00 1 REMARK REVDAT 1 08-AUG-18 6H00 0 JRNL AUTH S.MACKINNON,M.P.WILSON,L.SHRESTHA,G.A.BEZERRA,J.NEWMAN, JRNL AUTH 2 N.FOX,F.SORRELL,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA, JRNL AUTH 3 P.T.CLAYTON,P.B.MILLS,W.W.YUE JRNL TITL CRYSTAL STRUCTURE OF HUMAN PYRIDOXINE 5-PHOPHATE OXIDASE, JRNL TITL 2 R116Q VARIANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28380 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1418 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) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2077 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1629 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : 0.59000 REMARK 3 B12 (A**2) : -0.09000 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): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1760 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1585 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2390 ; 1.538 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3651 ; 0.944 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 210 ; 5.882 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;35.090 ;23.908 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 279 ;12.050 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;15.561 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 243 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1985 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 416 ; 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): 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): 3345 ; 2.216 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 17 ;26.553 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3330 ; 9.957 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 51 A 261 REMARK 3 ORIGIN FOR THE GROUP (A): -26.6633 -6.6947 -2.0380 REMARK 3 T TENSOR REMARK 3 T11: 0.0228 T22: 0.0204 REMARK 3 T33: 0.0112 T12: -0.0118 REMARK 3 T13: -0.0050 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 0.5006 L22: 2.0651 REMARK 3 L33: 1.3373 L12: -0.0098 REMARK 3 L13: 0.1407 L23: -0.0575 REMARK 3 S TENSOR REMARK 3 S11: 0.0289 S12: -0.0309 S13: 0.0063 REMARK 3 S21: 0.1944 S22: -0.0831 S23: -0.0699 REMARK 3 S31: 0.0611 S32: -0.0810 S33: 0.0542 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 : WITH TLS ADDED REMARK 4 REMARK 4 6H00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200010812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.23 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29800 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 34.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 1.05300 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: PHASER REMARK 200 STARTING MODEL: 1NRG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG1000, 0.2 M LITHIUM SULPHATE, REMARK 280 0.1 M CITRATE, PH 4.2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.64333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.28667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.28667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.64333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -19.64333 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 THR A 2 REMARK 465 CYS A 3 REMARK 465 TRP A 4 REMARK 465 LEU A 5 REMARK 465 ARG A 6 REMARK 465 GLY A 7 REMARK 465 VAL A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 THR A 11 REMARK 465 PHE A 12 REMARK 465 GLY A 13 REMARK 465 ARG A 14 REMARK 465 PRO A 15 REMARK 465 ALA A 16 REMARK 465 GLU A 17 REMARK 465 TRP A 18 REMARK 465 PRO A 19 REMARK 465 GLY A 20 REMARK 465 TYR A 21 REMARK 465 LEU A 22 REMARK 465 SER A 23 REMARK 465 HIS A 24 REMARK 465 LEU A 25 REMARK 465 CYS A 26 REMARK 465 GLY A 27 REMARK 465 ARG A 28 REMARK 465 SER A 29 REMARK 465 ALA A 30 REMARK 465 ALA A 31 REMARK 465 MET A 32 REMARK 465 ASP A 33 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 PRO A 36 REMARK 465 MET A 37 REMARK 465 ARG A 38 REMARK 465 LYS A 39 REMARK 465 SER A 40 REMARK 465 TYR A 41 REMARK 465 ARG A 42 REMARK 465 GLY A 43 REMARK 465 ASP A 44 REMARK 465 ARG A 45 REMARK 465 GLU A 46 REMARK 465 ALA A 47 REMARK 465 PHE A 48 REMARK 465 GLU A 49 REMARK 465 GLU A 50 REMARK 465 LEU A 236 REMARK 465 PRO A 237 REMARK 465 THR A 238 REMARK 465 GLY A 239 REMARK 465 ASP A 240 REMARK 465 SER A 241 REMARK 465 PRO A 242 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 THR A 51 OG1 CG2 REMARK 470 HIS A 52 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 60 CE NZ REMARK 470 ARG A 88 CD NE CZ NH1 NH2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 LYS A 119 NZ REMARK 470 LYS A 147 CE NZ REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 LYS A 163 NZ REMARK 470 HIS A 173 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 185 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 186 NZ REMARK 470 LYS A 204 CE NZ 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 LEU A 53 C LEU A 53 O -0.129 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 52 37.79 82.28 REMARK 500 ASN A 124 82.75 -150.27 REMARK 500 ARG A 225 -9.01 79.71 REMARK 500 GLU A 252 -125.86 51.37 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 308 DBREF 6H00 A 1 261 UNP Q9NVS9 PNPO_HUMAN 1 261 SEQADV 6H00 GLN A 116 UNP Q9NVS9 ARG 116 VARIANT SEQRES 1 A 261 MET THR CYS TRP LEU ARG GLY VAL THR ALA THR PHE GLY SEQRES 2 A 261 ARG PRO ALA GLU TRP PRO GLY TYR LEU SER HIS LEU CYS SEQRES 3 A 261 GLY ARG SER ALA ALA MET ASP LEU GLY PRO MET ARG LYS SEQRES 4 A 261 SER TYR ARG GLY ASP ARG GLU ALA PHE GLU GLU THR HIS SEQRES 5 A 261 LEU THR SER LEU ASP PRO VAL LYS GLN PHE ALA ALA TRP SEQRES 6 A 261 PHE GLU GLU ALA VAL GLN CYS PRO ASP ILE GLY GLU ALA SEQRES 7 A 261 ASN ALA MET CYS LEU ALA THR CYS THR ARG ASP GLY LYS SEQRES 8 A 261 PRO SER ALA ARG MET LEU LEU LEU LYS GLY PHE GLY LYS SEQRES 9 A 261 ASP GLY PHE ARG PHE PHE THR ASN PHE GLU SER GLN LYS SEQRES 10 A 261 GLY LYS GLU LEU ASP SER ASN PRO PHE ALA SER LEU VAL SEQRES 11 A 261 PHE TYR TRP GLU PRO LEU ASN ARG GLN VAL ARG VAL GLU SEQRES 12 A 261 GLY PRO VAL LYS LYS LEU PRO GLU GLU GLU ALA GLU CYS SEQRES 13 A 261 TYR PHE HIS SER ARG PRO LYS SER SER GLN ILE GLY ALA SEQRES 14 A 261 VAL VAL SER HIS GLN SER SER VAL ILE PRO ASP ARG GLU SEQRES 15 A 261 TYR LEU ARG LYS LYS ASN GLU GLU LEU GLU GLN LEU TYR SEQRES 16 A 261 GLN ASP GLN GLU VAL PRO LYS PRO LYS SER TRP GLY GLY SEQRES 17 A 261 TYR VAL LEU TYR PRO GLN VAL MET GLU PHE TRP GLN GLY SEQRES 18 A 261 GLN THR ASN ARG LEU HIS ASP ARG ILE VAL PHE ARG ARG SEQRES 19 A 261 GLY LEU PRO THR GLY ASP SER PRO LEU GLY PRO MET THR SEQRES 20 A 261 HIS ARG GLY GLU GLU ASP TRP LEU TYR GLU ARG LEU ALA SEQRES 21 A 261 PRO HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET FMN A 304 31 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HETNAM SO4 SULFATE ION HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 FMN C17 H21 N4 O9 P FORMUL 6 EDO 4(C2 H6 O2) FORMUL 10 HOH *45(H2 O) HELIX 1 AA1 ASP A 57 CYS A 72 1 16 HELIX 2 AA2 SER A 115 ASN A 124 1 10 HELIX 3 AA3 GLU A 134 LEU A 136 5 3 HELIX 4 AA4 PRO A 150 SER A 160 1 11 HELIX 5 AA5 PRO A 162 SER A 172 1 11 HELIX 6 AA6 ASP A 180 TYR A 195 1 16 SHEET 1 AA1 7 PRO A 92 LEU A 98 0 SHEET 2 AA1 7 ALA A 80 CYS A 86 -1 N LEU A 83 O ARG A 95 SHEET 3 AA1 7 PHE A 126 TRP A 133 -1 O SER A 128 N ALA A 84 SHEET 4 AA1 7 ARG A 138 LYS A 148 -1 O ARG A 138 N TRP A 133 SHEET 5 AA1 7 TRP A 206 LEU A 211 -1 O VAL A 210 N LYS A 147 SHEET 6 AA1 7 GLY A 106 ASN A 112 -1 N PHE A 107 O LEU A 211 SHEET 7 AA1 7 PHE A 102 GLY A 103 -1 N GLY A 103 O GLY A 106 SHEET 1 AA2 8 PRO A 92 LEU A 98 0 SHEET 2 AA2 8 ALA A 80 CYS A 86 -1 N LEU A 83 O ARG A 95 SHEET 3 AA2 8 PHE A 126 TRP A 133 -1 O SER A 128 N ALA A 84 SHEET 4 AA2 8 ARG A 138 LYS A 148 -1 O ARG A 138 N TRP A 133 SHEET 5 AA2 8 VAL A 215 GLN A 220 -1 O TRP A 219 N GLN A 139 SHEET 6 AA2 8 ASP A 228 ARG A 234 -1 O PHE A 232 N MET A 216 SHEET 7 AA2 8 TRP A 254 ARG A 258 -1 O GLU A 257 N VAL A 231 SHEET 8 AA2 8 HIS A 248 ARG A 249 -1 N HIS A 248 O TYR A 256 SITE 1 AC1 4 LYS A 100 ARG A 161 SER A 165 ARG A 225 SITE 1 AC2 6 GLN A 71 VAL A 170 VAL A 171 SER A 172 SITE 2 AC2 6 HIS A 173 HOH A 434 SITE 1 AC3 3 THR A 247 HIS A 248 ARG A 249 SITE 1 AC4 20 GLU A 77 ARG A 95 MET A 96 LEU A 97 SITE 2 AC4 20 LEU A 98 PHE A 110 THR A 111 SER A 115 SITE 3 AC4 20 GLN A 116 LYS A 117 TYR A 132 GLN A 139 SITE 4 AC4 20 ARG A 141 GLN A 174 SER A 175 TRP A 219 SITE 5 AC4 20 ARG A 229 HOH A 401 HOH A 412 HOH A 419 SITE 1 AC5 6 LEU A 121 ASP A 122 VAL A 146 LYS A 147 SITE 2 AC5 6 LYS A 148 EDO A 306 SITE 1 AC6 2 LYS A 148 EDO A 305 SITE 1 AC7 6 HIS A 52 LEU A 53 THR A 54 GLN A 61 SITE 2 AC7 6 TRP A 65 ARG A 138 SITE 1 AC8 6 GLU A 77 ALA A 78 ALA A 80 TYR A 132 SITE 2 AC8 6 TRP A 133 GLU A 134 CRYST1 83.330 83.330 58.930 90.00 90.00 120.00 P 31 2 1 6 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 0.012000 0.006928 0.000000 0.00000 SCALE2 0.000000 0.013857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016969 0.00000