HEADER HYDROLASE 02-JUL-15 5CCY TITLE 2009 H1N1 PA ENDONUCLEASE IN COMPLEX WITH DTMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYMERASE ACIDIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ENDONUCLEASE DOMAIN (UNP RESIDUES 1-50, 73-196); COMPND 5 SYNONYM: PA; COMPND 6 EC: 3.1.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 3 ORGANISM_TAXID: 641501; SOURCE 4 STRAIN: SWL A/CALIFORNIA/04/2009 H1N1; SOURCE 5 GENE: PA; 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_PLASMID: PET52B KEYWDS INFLUENZA, RESISTANCE, ENDONUCLEASE, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.KUMAR,S.W.WHITE REVDAT 7 27-SEP-23 5CCY 1 LINK REVDAT 6 08-JAN-20 5CCY 1 REMARK REVDAT 5 11-DEC-19 5CCY 1 REMARK REVDAT 4 06-SEP-17 5CCY 1 JRNL REMARK REVDAT 3 13-APR-16 5CCY 1 JRNL REVDAT 2 30-MAR-16 5CCY 1 JRNL REVDAT 1 16-MAR-16 5CCY 0 JRNL AUTH M.S.SONG,G.KUMAR,W.R.SHADRICK,W.ZHOU,T.JEEVAN,Z.LI, JRNL AUTH 2 P.J.SLAVISH,T.P.FABRIZIO,S.W.YOON,T.R.WEBB,R.J.WEBBY, JRNL AUTH 3 S.W.WHITE JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF INFLUENZA VARIANTS JRNL TITL 2 RESISTANT TO A VIRAL ENDONUCLEASE INHIBITOR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 3669 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 26976575 JRNL DOI 10.1073/PNAS.1519772113 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12084 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 623 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 847 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1458 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : 1.51000 REMARK 3 B12 (A**2) : -0.23000 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): 0.190 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.978 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1510 ; 0.025 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1409 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2033 ; 2.198 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3240 ; 1.194 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 177 ; 6.372 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;37.495 ;23.026 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 275 ;15.914 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.032 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 217 ; 0.162 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1672 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 364 ; 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): 711 ; 2.221 ; 2.748 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 710 ; 2.216 ; 2.746 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 887 ; 3.295 ; 4.105 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 178 REMARK 3 RESIDUE RANGE : A 201 A 203 REMARK 3 ORIGIN FOR THE GROUP (A): -14.2484 75.4169 14.1762 REMARK 3 T TENSOR REMARK 3 T11: 0.0906 T22: 0.0221 REMARK 3 T33: 0.0528 T12: 0.0021 REMARK 3 T13: 0.0418 T23: -0.0217 REMARK 3 L TENSOR REMARK 3 L11: 0.1490 L22: 0.9800 REMARK 3 L33: 1.4334 L12: -0.1455 REMARK 3 L13: -0.1227 L23: 0.4831 REMARK 3 S TENSOR REMARK 3 S11: -0.0646 S12: -0.0017 S13: -0.0501 REMARK 3 S21: -0.0003 S22: -0.0586 S23: 0.0465 REMARK 3 S31: 0.1418 S32: -0.0208 S33: 0.1232 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 : WITH TLS ADDED REMARK 4 REMARK 4 5CCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12747 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 64.006 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 28.40 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 28.10 REMARK 200 R MERGE FOR SHELL (I) : 0.96500 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: PDB ENTRY 4E5E REMARK 200 REMARK 200 REMARK: HEXAGONAL PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 5 MM REMARK 280 MANGANESE CHLORIDE, 0.1 M TRIS, PH 8.5, 30% W/V PEG4000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 42.76067 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 85.52133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.76067 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 85.52133 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.76067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 85.52133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 42.76067 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 85.52133 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: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 ALA A 198 REMARK 465 ALA A 199 REMARK 465 GLU A 200 REMARK 465 LEU A 201 REMARK 465 ALA A 202 REMARK 465 LEU A 203 REMARK 465 VAL A 204 REMARK 465 PRO A 205 REMARK 465 ARG A 206 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 GLU A 101 CG CD OE1 OE2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 GLU A 141 CG CD OE1 OE2 REMARK 470 LYS A 142 CG CD 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 MET A 1 N MET A 1 CA 0.129 REMARK 500 GLU A 18 CD GLU A 18 OE2 -0.097 REMARK 500 TYR A 24 CG TYR A 24 CD2 0.097 REMARK 500 TYR A 24 CE1 TYR A 24 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 ASP A 83 CB - CG - OD1 ANGL. DEV. = 11.4 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 196 NE - CZ - NH1 ANGL. DEV. = 3.8 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 ARG A 125 -112.66 -101.26 REMARK 500 LYS A 139 -55.46 68.55 REMARK 500 THR A 162 -58.10 72.72 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 A 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 NE2 REMARK 620 2 ASP A 108 OD2 97.7 REMARK 620 3 GLU A 119 OE2 168.0 89.1 REMARK 620 4 ILE A 120 O 86.9 92.6 82.9 REMARK 620 5 TMP A 303 O2P 88.5 104.4 99.4 162.8 REMARK 620 6 TMP A 303 O1P 89.9 168.3 85.0 96.8 66.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 80 OE2 REMARK 620 2 ASP A 108 OD1 89.9 REMARK 620 3 TMP A 303 O2P 94.9 91.6 REMARK 620 4 HOH A 404 O 173.0 85.8 90.8 REMARK 620 5 HOH A 445 O 87.7 86.0 176.5 86.4 REMARK 620 6 HOH A 473 O 92.1 174.9 92.9 91.8 89.4 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 MN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TMP A 303 DBREF 5CCY A 1 50 UNP C3W5S0 C3W5S0_I09A0 1 50 DBREF 5CCY A 73 196 UNP C3W5S0 C3W5S0_I09A0 73 196 SEQADV 5CCY GLY A 51 UNP C3W5S0 LINKER SEQADV 5CCY GLY A 52 UNP C3W5S0 LINKER SEQADV 5CCY SER A 53 UNP C3W5S0 LINKER SEQADV 5CCY ALA A 197 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY ALA A 198 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY ALA A 199 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY GLU A 200 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY LEU A 201 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY ALA A 202 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY LEU A 203 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY VAL A 204 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY PRO A 205 UNP C3W5S0 EXPRESSION TAG SEQADV 5CCY ARG A 206 UNP C3W5S0 EXPRESSION TAG SEQRES 1 A 187 MET GLU ASP PHE VAL ARG GLN CYS PHE ASN PRO MET ILE SEQRES 2 A 187 VAL GLU LEU ALA GLU LYS ALA MET LYS GLU TYR GLY GLU SEQRES 3 A 187 ASP PRO LYS ILE GLU THR ASN LYS PHE ALA ALA ILE CYS SEQRES 4 A 187 THR HIS LEU GLU VAL CYS PHE MET TYR SER ASP GLY GLY SEQRES 5 A 187 SER LYS HIS ARG PHE GLU ILE ILE GLU GLY ARG ASP ARG SEQRES 6 A 187 ILE MET ALA TRP THR VAL VAL ASN SER ILE CYS ASN THR SEQRES 7 A 187 THR GLY VAL GLU LYS PRO LYS PHE LEU PRO ASP LEU TYR SEQRES 8 A 187 ASP TYR LYS GLU ASN ARG PHE ILE GLU ILE GLY VAL THR SEQRES 9 A 187 ARG ARG GLU VAL HIS ILE TYR TYR LEU GLU LYS ALA ASN SEQRES 10 A 187 LYS ILE LYS SER GLU LYS THR HIS ILE HIS ILE PHE SER SEQRES 11 A 187 PHE THR GLY GLU GLU MET ALA THR LYS ALA ASP TYR THR SEQRES 12 A 187 LEU ASP GLU GLU SER ARG ALA ARG ILE LYS THR ARG LEU SEQRES 13 A 187 PHE THR ILE ARG GLN GLU MET ALA SER ARG SER LEU TRP SEQRES 14 A 187 ASP SER PHE ARG GLN SER GLU ARG ALA ALA ALA GLU LEU SEQRES 15 A 187 ALA LEU VAL PRO ARG HET MN A 301 1 HET MN A 302 1 HET TMP A 303 21 HETNAM MN MANGANESE (II) ION HETNAM TMP THYMIDINE-5'-PHOSPHATE FORMUL 2 MN 2(MN 2+) FORMUL 4 TMP C10 H15 N2 O8 P FORMUL 5 HOH *88(H2 O) HELIX 1 AA1 MET A 1 PHE A 9 1 9 HELIX 2 AA2 ASN A 10 TYR A 24 1 15 HELIX 3 AA3 GLU A 31 ASP A 50 1 20 HELIX 4 AA4 ASP A 83 GLY A 99 1 17 HELIX 5 AA5 GLU A 126 LYS A 139 1 14 HELIX 6 AA6 LYS A 158 ASP A 160 5 3 HELIX 7 AA7 ASP A 164 ARG A 185 1 22 HELIX 8 AA8 LEU A 187 GLN A 193 1 7 SHEET 1 AA1 5 PHE A 76 ILE A 78 0 SHEET 2 AA1 5 LEU A 109 ASP A 111 -1 O TYR A 110 N GLU A 77 SHEET 3 AA1 5 ARG A 116 THR A 123 -1 O ARG A 116 N ASP A 111 SHEET 4 AA1 5 HIS A 144 SER A 149 1 O HIS A 144 N GLU A 119 SHEET 5 AA1 5 GLU A 154 ALA A 156 -1 O MET A 155 N ILE A 147 LINK NE2 HIS A 41 MN MN A 301 1555 1555 2.26 LINK OE2 GLU A 80 MN MN A 302 1555 1555 2.14 LINK OD2 ASP A 108 MN MN A 301 1555 1555 2.14 LINK OD1 ASP A 108 MN MN A 302 1555 1555 2.16 LINK OE2 GLU A 119 MN MN A 301 1555 1555 2.24 LINK O ILE A 120 MN MN A 301 1555 1555 2.13 LINK MN MN A 301 O2P TMP A 303 1555 1555 2.21 LINK MN MN A 301 O1P TMP A 303 1555 1555 2.25 LINK MN MN A 302 O2P TMP A 303 1555 1555 2.11 LINK MN MN A 302 O HOH A 404 1555 1555 2.18 LINK MN MN A 302 O HOH A 445 1555 1555 2.25 LINK MN MN A 302 O HOH A 473 1555 1555 2.21 SITE 1 AC1 5 HIS A 41 ASP A 108 GLU A 119 ILE A 120 SITE 2 AC1 5 TMP A 303 SITE 1 AC2 6 GLU A 80 ASP A 108 TMP A 303 HOH A 404 SITE 2 AC2 6 HOH A 445 HOH A 473 SITE 1 AC3 17 TYR A 24 LYS A 34 HIS A 41 GLU A 80 SITE 2 AC3 17 ASP A 108 GLU A 119 ILE A 120 LYS A 134 SITE 3 AC3 17 MN A 301 MN A 302 HOH A 404 HOH A 412 SITE 4 AC3 17 HOH A 431 HOH A 439 HOH A 444 HOH A 449 SITE 5 AC3 17 HOH A 462 CRYST1 73.908 73.908 128.282 90.00 90.00 120.00 P 64 2 2 12 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 0.013530 0.007812 0.000000 0.00000 SCALE2 0.000000 0.015623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007795 0.00000