HEADER HYDROLASE 12-DEC-16 5U7X TITLE CRYSTAL STRUCTURE OF A NUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE TITLE 2 (NTPDASE) FROM THE LEGUME VIGNA UNGUICULATA SUBSP. CYLINDRICA TITLE 3 (DOLICHOS BIFLORUS) IN COMPLEX WITH PHOSPHATE AND MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NOD FACTOR BINDING LECTIN-NUCLEOTIDE PHOSPHOHYDROLASE; COMPND 3 CHAIN: F; COMPND 4 FRAGMENT: RESIDUES 49-462; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIGNA UNGUICULATA SUBSP. CYLINDRICA; SOURCE 3 ORGANISM_COMMON: HORSE GRAM; SOURCE 4 ORGANISM_TAXID: 3840; SOURCE 5 GENE: LNP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS APYRASE, NTPDASE, RNASE-H FOLD, MIXED 5 STRAND BETA-SHEET, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.H.CUMMING,E.L.SUMMERS,T.OULAVALLICKAL,N.ROBERTS,V.L.ARCUS REVDAT 5 04-OCT-23 5U7X 1 LINK REVDAT 4 02-AUG-17 5U7X 1 JRNL REVDAT 3 14-JUN-17 5U7X 1 JRNL REVDAT 2 07-JUN-17 5U7X 1 JRNL REVDAT 1 31-MAY-17 5U7X 0 JRNL AUTH E.L.SUMMERS,M.H.CUMMING,T.OULAVALLICKAL,N.J.ROBERTS, JRNL AUTH 2 V.L.ARCUS JRNL TITL STRUCTURES AND KINETICS FOR PLANT NUCLEOSIDE TRIPHOSPHATE JRNL TITL 2 DIPHOSPHOHYDROLASES SUPPORT A DOMAIN MOTION CATALYTIC JRNL TITL 3 MECHANISM. JRNL REF PROTEIN SCI. V. 26 1627 2017 JRNL REFN ESSN 1469-896X JRNL PMID 28543850 JRNL DOI 10.1002/PRO.3199 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15045 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 789 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1103 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3147 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.01000 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): 0.591 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.307 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.207 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.473 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3230 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2992 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4397 ; 1.890 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6885 ; 0.903 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 411 ; 7.356 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;35.939 ;24.610 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 503 ;18.388 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.289 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 487 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3702 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 718 ; 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): 1647 ; 1.925 ; 3.039 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1646 ; 1.923 ; 3.038 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2057 ; 3.019 ; 4.554 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2058 ; 3.018 ; 4.555 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1583 ; 2.528 ; 3.264 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1576 ; 2.525 ; 3.265 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2329 ; 4.018 ; 4.793 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3687 ; 5.724 ;24.172 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3655 ; 5.668 ;24.187 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 : 2 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 : F 3 F 126 REMARK 3 ORIGIN FOR THE GROUP (A): -4.2454 18.6782 14.1873 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: -0.0000 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 127 F 414 REMARK 3 ORIGIN FOR THE GROUP (A): -21.6594 34.5665 12.4487 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: -0.0000 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 REMARK 4 REMARK 4 5U7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15843 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 46.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.35300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5U7P REMARK 200 REMARK 200 REMARK: LARGE ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 50 MM ACETATE, PH 5.0, 9 REMARK 280 -12% MPD, 10-2-% PEG 3350, 5 MM AMP, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 60.04500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.55500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.04500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.55500 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: 650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 F -21 REMARK 465 GLY F -20 REMARK 465 SER F -19 REMARK 465 SER F -18 REMARK 465 HIS F -17 REMARK 465 HIS F -16 REMARK 465 HIS F -15 REMARK 465 HIS F -14 REMARK 465 HIS F -13 REMARK 465 HIS F -12 REMARK 465 SER F -11 REMARK 465 SER F -10 REMARK 465 GLY F -9 REMARK 465 LEU F -8 REMARK 465 VAL F -7 REMARK 465 PRO F -6 REMARK 465 ARG F -5 REMARK 465 GLY F -4 REMARK 465 SER F -3 REMARK 465 HIS F -2 REMARK 465 MET F -1 REMARK 465 SER F 0 REMARK 465 MET F 1 REMARK 465 GLU F 2 REMARK 465 ILE F 415 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 ASN F 36 CG OD1 ND2 REMARK 470 LYS F 57 CD CE NZ REMARK 470 ASP F 95 CB CG OD1 OD2 REMARK 470 LYS F 101 CD CE NZ REMARK 470 LYS F 176 CB CG CD CE NZ REMARK 470 LYS F 180 CG CD CE NZ REMARK 470 GLN F 183 CB CG CD OE1 NE2 REMARK 470 LYS F 191 CG CD CE NZ REMARK 470 LYS F 195 CE NZ REMARK 470 LYS F 198 CG CD CE NZ REMARK 470 LYS F 293 CG CD CE NZ REMARK 470 LYS F 317 CD CE NZ REMARK 470 LYS F 347 CG CD CE NZ REMARK 470 LYS F 407 CG CD CE NZ 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 F 678 O HOH F 723 1.86 REMARK 500 O HOH F 626 O HOH F 728 2.02 REMARK 500 O ASP F 71 O HOH F 601 2.02 REMARK 500 O HOH F 601 O HOH F 689 2.03 REMARK 500 O HOH F 605 O HOH F 672 2.11 REMARK 500 O HOH F 696 O HOH F 717 2.16 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 GLY F 233 C GLY F 233 O 0.136 REMARK 500 ASP F 236 CB ASP F 236 CG 0.156 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 ASP F 71 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP F 236 CB - CG - OD1 ANGL. DEV. = 14.4 DEGREES REMARK 500 ASP F 236 CB - CG - OD2 ANGL. DEV. = -5.6 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 THR F 88 -134.26 -122.01 REMARK 500 PRO F 182 -161.31 -73.62 REMARK 500 GLN F 183 -123.99 43.86 REMARK 500 THR F 279 -76.16 -98.66 REMARK 500 SER F 299 -110.41 66.84 REMARK 500 PHE F 342 67.32 -116.75 REMARK 500 GLN F 385 -119.81 53.94 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 ASP F 95 GLY F 96 141.83 REMARK 500 GLY F 224 ALA F 225 -149.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN F 503 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PO4 F 502 O1 REMARK 620 2 HOH F 609 O 72.1 REMARK 620 3 HOH F 621 O 88.2 158.4 REMARK 620 4 HOH F 625 O 91.6 82.5 89.4 REMARK 620 5 HOH F 663 O 88.6 99.6 88.4 177.8 REMARK 620 6 HOH F 668 O 173.9 101.9 97.4 86.1 94.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 F 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 F 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN F 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U7W RELATED DB: PDB REMARK 900 RELATED ID: 5U7V RELATED DB: PDB REMARK 900 RELATED ID: 5U7P RELATED DB: PDB DBREF 5U7X F 2 415 UNP Q9XFC9 Q9XFC9_VIGUC 49 462 SEQADV 5U7X MET F -21 UNP Q9XFC9 INITIATING METHIONINE SEQADV 5U7X GLY F -20 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X SER F -19 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X SER F -18 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X HIS F -17 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X HIS F -16 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X HIS F -15 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X HIS F -14 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X HIS F -13 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X HIS F -12 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X SER F -11 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X SER F -10 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X GLY F -9 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X LEU F -8 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X VAL F -7 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X PRO F -6 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X ARG F -5 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X GLY F -4 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X SER F -3 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X HIS F -2 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X MET F -1 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X SER F 0 UNP Q9XFC9 EXPRESSION TAG SEQADV 5U7X MET F 1 UNP Q9XFC9 EXPRESSION TAG SEQRES 1 F 437 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 F 437 LEU VAL PRO ARG GLY SER HIS MET SER MET GLU LEU LEU SEQRES 3 F 437 THR SER TYR ALA VAL ILE PHE ASP ALA GLY SER SER GLY SEQRES 4 F 437 SER ARG VAL HIS VAL PHE ASN PHE ASP GLN ASN LEU ASP SEQRES 5 F 437 LEU LEU HIS ILE GLY ASN ASP LEU GLU PHE THR LYS LYS SEQRES 6 F 437 ILE LYS PRO GLY LEU SER SER TYR ALA ASP LYS PRO GLU SEQRES 7 F 437 LYS ALA ALA GLU SER LEU ILE PRO LEU LEU GLU GLU ALA SEQRES 8 F 437 GLU ASP VAL VAL PRO GLU GLU LEU HIS PRO LYS THR PRO SEQRES 9 F 437 LEU LYS LEU GLY ALA THR ALA GLY LEU ARG LEU LEU ASP SEQRES 10 F 437 GLY ASP ALA ALA GLU LYS ILE LEU GLN ALA VAL ARG GLU SEQRES 11 F 437 MET PHE ARG ASN ARG SER SER LEU SER VAL GLN PRO ASP SEQRES 12 F 437 ALA VAL SER VAL ILE ASP GLY THR GLN GLU GLY SER TYR SEQRES 13 F 437 LEU TRP VAL THR VAL ASN TYR LEU LEU GLY LYS LEU GLY SEQRES 14 F 437 LYS LYS PHE THR LYS THR VAL GLY VAL ILE ASP LEU GLY SEQRES 15 F 437 GLY ALA SER VAL GLN MET ALA TYR ALA VAL SER ARG ASN SEQRES 16 F 437 THR ALA LYS ASN ALA PRO LYS PRO PRO GLN GLY GLU ASP SEQRES 17 F 437 PRO TYR MET LYS LYS LEU VAL LEU LYS GLY LYS LYS TYR SEQRES 18 F 437 ASP LEU TYR VAL HIS SER TYR LEU ARG TYR GLY ASN ASP SEQRES 19 F 437 ALA ALA ARG VAL LYS ILE PHE LYS THR THR ASP GLY ALA SEQRES 20 F 437 ALA SER PRO CYS LEU LEU ALA GLY TYR GLU ASP ILE TYR SEQRES 21 F 437 ARG TYR SER GLY GLU SER TYR ASN ILE TYR GLY PRO THR SEQRES 22 F 437 SER GLY ALA ASN PHE ASN GLU CYS ARG ASP LEU ALA LEU SEQRES 23 F 437 GLN ILE LEU ARG LEU ASN GLU PRO CYS SER HIS GLU ASN SEQRES 24 F 437 CYS THR PHE GLY GLY ILE TRP ASP GLY GLY LYS GLY SER SEQRES 25 F 437 GLY GLN LYS ASN LEU VAL VAL THR SER ALA PHE TYR TYR SEQRES 26 F 437 ARG SER SER GLU VAL GLY PHE VAL THR PRO PRO ASN SER SEQRES 27 F 437 LYS ASN ARG PRO LEU ASP PHE GLU THR ALA ALA LYS GLN SEQRES 28 F 437 ALA CYS SER LEU THR PHE GLU GLU ALA LYS SER THR PHE SEQRES 29 F 437 PRO ASN VAL GLU LYS ASP LYS LEU PRO PHE VAL CYS VAL SEQRES 30 F 437 ASP PHE THR TYR GLN TYR THR LEU LEU VAL ASP GLY PHE SEQRES 31 F 437 GLY LEU ASP PRO GLU GLN GLU ILE THR VAL ALA GLU GLY SEQRES 32 F 437 ILE GLU TYR GLN ASP ALA ILE VAL GLU THR ALA TRP PRO SEQRES 33 F 437 LEU GLY THR ALA ILE GLU ALA ILE SER SER LEU PRO LYS SEQRES 34 F 437 PHE ASN ARG LEU MET TYR PHE ILE HET PO4 F 501 5 HET PO4 F 502 5 HET MN F 503 1 HETNAM PO4 PHOSPHATE ION HETNAM MN MANGANESE (II) ION FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 MN MN 2+ FORMUL 5 HOH *137(H2 O) HELIX 1 AA1 GLY F 47 ALA F 52 5 6 HELIX 2 AA2 LYS F 54 LEU F 62 1 9 HELIX 3 AA3 LEU F 62 VAL F 73 1 12 HELIX 4 AA4 PRO F 74 LYS F 80 5 7 HELIX 5 AA5 THR F 88 LEU F 93 1 6 HELIX 6 AA6 GLY F 96 SER F 114 1 19 HELIX 7 AA7 ASP F 127 LEU F 143 1 17 HELIX 8 AA8 LYS F 149 THR F 153 5 5 HELIX 9 AA9 SER F 171 ASN F 177 1 7 HELIX 10 AB1 GLY F 210 THR F 221 1 12 HELIX 11 AB2 ASN F 255 LEU F 267 1 13 HELIX 12 AB3 GLY F 289 LYS F 293 5 5 HELIX 13 AB4 ALA F 300 GLY F 309 1 10 HELIX 14 AB5 PRO F 320 SER F 332 1 13 HELIX 15 AB6 THR F 334 PHE F 342 1 9 HELIX 16 AB7 LYS F 349 PRO F 351 5 3 HELIX 17 AB8 PHE F 352 ASP F 366 1 15 HELIX 18 AB9 TRP F 393 SER F 403 1 11 SHEET 1 AA1 5 PHE F 40 ILE F 44 0 SHEET 2 AA1 5 SER F 18 ASP F 26 -1 N VAL F 22 O PHE F 40 SHEET 3 AA1 5 THR F 5 ALA F 13 -1 N ASP F 12 O ARG F 19 SHEET 4 AA1 5 PRO F 82 ALA F 87 1 O GLY F 86 N PHE F 11 SHEET 5 AA1 5 SER F 117 VAL F 125 1 O ALA F 122 N LEU F 85 SHEET 1 AA2 8 ASN F 315 ASN F 318 0 SHEET 2 AA2 8 ILE F 376 ALA F 379 -1 O ILE F 376 N ASN F 318 SHEET 3 AA2 8 LEU F 295 SER F 299 1 N VAL F 297 O THR F 377 SHEET 4 AA2 8 GLY F 155 LEU F 159 1 N ILE F 157 O THR F 298 SHEET 5 AA2 8 SER F 163 VAL F 170 -1 O GLN F 165 N ASP F 158 SHEET 6 AA2 8 LYS F 197 LEU F 207 -1 O HIS F 204 N MET F 166 SHEET 7 AA2 8 MET F 189 LEU F 194 -1 N LEU F 192 O TYR F 199 SHEET 8 AA2 8 MET F 412 TYR F 413 -1 O TYR F 413 N VAL F 193 SHEET 1 AA3 2 GLU F 235 TYR F 240 0 SHEET 2 AA3 2 GLU F 243 TYR F 248 -1 O GLU F 243 N TYR F 240 SHEET 1 AA4 2 GLY F 381 TYR F 384 0 SHEET 2 AA4 2 ALA F 387 GLU F 390 -1 O ALA F 387 N TYR F 384 SSBOND 1 CYS F 229 CYS F 259 1555 1555 2.05 SSBOND 2 CYS F 273 CYS F 278 1555 1555 2.06 SSBOND 3 CYS F 331 CYS F 354 1555 1555 2.02 LINK O1 PO4 F 502 MN MN F 503 1555 1555 2.24 LINK MN MN F 503 O HOH F 609 1555 1555 1.96 LINK MN MN F 503 O HOH F 621 1555 1555 2.14 LINK MN MN F 503 O HOH F 625 1555 1555 2.18 LINK MN MN F 503 O HOH F 663 1555 1555 2.25 LINK MN MN F 503 O HOH F 668 1555 1555 2.35 CISPEP 1 LYS F 45 PRO F 46 0 -0.30 CISPEP 2 GLN F 183 GLY F 184 0 -18.99 CISPEP 3 GLU F 276 ASN F 277 0 -6.60 CISPEP 4 PRO F 313 PRO F 314 0 3.90 SITE 1 AC1 4 ARG F 19 LYS F 43 TYR F 303 GLU F 390 SITE 1 AC2 11 GLY F 14 SER F 15 THR F 88 ALA F 89 SITE 2 AC2 11 GLY F 160 GLY F 161 ALA F 162 SER F 163 SITE 3 AC2 11 MN F 503 HOH F 609 HOH F 621 SITE 1 AC3 6 PO4 F 502 HOH F 609 HOH F 621 HOH F 625 SITE 2 AC3 6 HOH F 663 HOH F 668 CRYST1 120.090 71.110 93.270 90.00 139.45 90.00 C 1 2 1 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 0.008327 0.000000 0.009733 0.00000 SCALE2 0.000000 0.014063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016492 0.00000