HEADER HYDROLASE 08-SEP-11 3TPY TITLE CRYSTAL STRUCTURE OF M-PMV DUTPASE WITH A MIXED POPULATION OF TITLE 2 SUBSTRATE (DUPNPP) AND POST-INVERSION PRODUCT (DUMP) IN THE ACTIVE TITLE 3 SITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DUTPASE (CATALYTIC) DOMAIN, UNP RESIDUES 608-759; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MASON-PFIZER MONKEY VIRUS; SOURCE 3 ORGANISM_COMMON: MPMV; SOURCE 4 ORGANISM_TAXID: 11855; SOURCE 5 GENE: GAG-PRO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS JELLY ROLL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR O.BARABAS,V.NEMETH,B.G.VERTESSY REVDAT 4 13-SEP-23 3TPY 1 REMARK SEQADV LINK REVDAT 3 24-JAN-18 3TPY 1 JRNL REVDAT 2 08-NOV-17 3TPY 1 REMARK REVDAT 1 12-OCT-11 3TPY 0 JRNL AUTH O.BARABAS,V.NEMETH,A.BODOR,A.PERCZEL,E.ROSTA,Z.KELE, JRNL AUTH 2 I.ZAGYVA,Z.SZABADKA,V.I.GROLMUSZ,M.WILMANNS,B.G.VERTESSY JRNL TITL STRUCTURAL SNAPSHOTS OF ENZYME-CATALYSED PHOSPHATE ESTER JRNL TITL 2 HYDROLYSIS DIRECTLY VISUALIZE IN-LINE ATTACK AND INVERSION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.BARABAS,V.NEMETH,B.G.VERTESSY REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF DUTPASE REMARK 1 TITL 2 FROM MASON-PFIZER MONKEY RETROVIRUS. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 62 399 2006 REMARK 1 REFN ESSN 1744-3091 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 12600 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 705 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 908 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 831 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79000 REMARK 3 B22 (A**2) : 0.79000 REMARK 3 B33 (A**2) : -1.19000 REMARK 3 B12 (A**2) : 0.40000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.480 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 921 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1266 ; 1.957 ; 2.085 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 114 ; 5.745 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 26 ;35.517 ;25.769 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 155 ;15.274 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;28.651 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 158 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 630 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 427 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 642 ; 0.325 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 107 ; 0.178 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.099 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 93 ; 0.261 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.170 ; 0.200 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): 578 ; 2.722 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 939 ; 3.509 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 370 ; 6.941 ;10.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 326 ; 9.959 ;50.000 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 : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 24 A 136 REMARK 3 RESIDUE RANGE : A 777 A 777 REMARK 3 RESIDUE RANGE : A 999 A 999 REMARK 3 ORIGIN FOR THE GROUP (A): 2.4828 58.4914 30.3186 REMARK 3 T TENSOR REMARK 3 T11: -0.0134 T22: -0.0332 REMARK 3 T33: 0.0000 T12: -0.0020 REMARK 3 T13: -0.0037 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 0.3333 L22: 0.5083 REMARK 3 L33: 1.2644 L12: -0.0124 REMARK 3 L13: -0.3999 L23: 0.1761 REMARK 3 S TENSOR REMARK 3 S11: 0.0153 S12: -0.0398 S13: -0.1026 REMARK 3 S21: -0.0033 S22: 0.0321 S23: 0.0370 REMARK 3 S31: 0.0352 S32: 0.0322 S33: -0.0474 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3TPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-03; 18-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG; ESRF REMARK 200 BEAMLINE : X13; ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8028; 1.0720 REMARK 200 MONOCHROMATOR : SI [111], HORIZONTALLY FOCUSING; REMARK 200 NULL REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM; ADSC QUANTUM REMARK 200 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13399 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 44.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: PDB ENTRY 2D4L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM CHLORIDE, TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -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 0.00000 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 0.00000 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 31.81750 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 31.81750 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 31.81750 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 -0.500000 -0.866025 0.000000 60.55900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 104.89126 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -60.55900 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 104.89126 REMARK 350 BIOMT3 3 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 N TRS A 153 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 255 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 LYS A 1 REMARK 465 ARG A 2 REMARK 465 VAL A 3 REMARK 465 GLU A 4 REMARK 465 GLY A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 PRO A 8 REMARK 465 GLY A 9 REMARK 465 PRO A 10 REMARK 465 GLU A 11 REMARK 465 THR A 12 REMARK 465 SER A 13 REMARK 465 LEU A 14 REMARK 465 TRP A 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 GLN A 18 REMARK 465 LEU A 19 REMARK 465 CYS A 20 REMARK 465 SER A 21 REMARK 465 SER A 22 REMARK 465 GLN A 23 REMARK 465 GLN A 137 REMARK 465 GLN A 138 REMARK 465 PRO A 139 REMARK 465 TYR A 140 REMARK 465 ARG A 141 REMARK 465 GLY A 142 REMARK 465 GLN A 143 REMARK 465 GLY A 144 REMARK 465 SER A 145 REMARK 465 PHE A 146 REMARK 465 GLY A 147 REMARK 465 SER A 148 REMARK 465 SER A 149 REMARK 465 ASP A 150 REMARK 465 ILE A 151 REMARK 465 TYR A 152 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 GLN A 24 CD OE1 NE2 REMARK 470 LYS A 85 CE NZ REMARK 470 LYS A 135 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 GLY A 37 O HOH A 230 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 45 CB SER A 45 OG 0.082 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 MG A 999 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UMP A 154 OP1 REMARK 620 2 HOH A 223 O 142.7 REMARK 620 3 HOH A 225 O 122.9 87.0 REMARK 620 4 HOH A 245 O 120.6 75.5 91.2 REMARK 620 5 DUP A 777 O2G 67.8 97.2 84.1 171.5 REMARK 620 6 DUP A 777 O1A 25.7 167.9 100.8 113.2 74.6 REMARK 620 7 DUP A 777 O1B 59.6 87.2 169.9 95.3 88.5 83.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 777 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMP A 154 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D4N RELATED DB: PDB REMARK 900 RELATED ID: 2D4L RELATED DB: PDB REMARK 900 RELATED ID: 2D4M RELATED DB: PDB REMARK 900 RELATED ID: 3TP1 RELATED DB: PDB REMARK 900 RELATED ID: 3TPN RELATED DB: PDB REMARK 900 RELATED ID: 3TPS RELATED DB: PDB REMARK 900 RELATED ID: 3TPW RELATED DB: PDB REMARK 900 RELATED ID: 3TQ3 RELATED DB: PDB REMARK 900 RELATED ID: 3TQ4 RELATED DB: PDB REMARK 900 RELATED ID: 3TQ5 RELATED DB: PDB REMARK 900 RELATED ID: 3TRL RELATED DB: PDB REMARK 900 RELATED ID: 3TRN RELATED DB: PDB REMARK 900 RELATED ID: 3TS6 RELATED DB: PDB REMARK 900 RELATED ID: 3TSL RELATED DB: PDB REMARK 900 RELATED ID: 3TTA RELATED DB: PDB DBREF 3TPY A 1 152 UNP O92810 O92810_MPMV 608 759 SEQADV 3TPY LYS A 1 UNP O92810 ASN 608 ENGINEERED MUTATION SEQRES 1 A 152 LYS ARG VAL GLU GLY PRO ALA PRO GLY PRO GLU THR SER SEQRES 2 A 152 LEU TRP GLY SER GLN LEU CYS SER SER GLN GLN LYS GLN SEQRES 3 A 152 PRO ILE SER LYS LEU THR ARG ALA THR PRO GLY SER ALA SEQRES 4 A 152 GLY LEU ASP LEU CYS SER THR SER HIS THR VAL LEU THR SEQRES 5 A 152 PRO GLU MET GLY PRO GLN ALA LEU SER THR GLY ILE TYR SEQRES 6 A 152 GLY PRO LEU PRO PRO ASN THR PHE GLY LEU ILE LEU GLY SEQRES 7 A 152 ARG SER SER ILE THR MET LYS GLY LEU GLN VAL TYR PRO SEQRES 8 A 152 GLY VAL ILE ASP ASN ASP TYR THR GLY GLU ILE LYS ILE SEQRES 9 A 152 MET ALA LYS ALA VAL ASN ASN ILE VAL THR VAL SER GLN SEQRES 10 A 152 GLY ASN ARG ILE ALA GLN LEU ILE LEU LEU PRO LEU ILE SEQRES 11 A 152 GLU THR ASP ASN LYS VAL GLN GLN PRO TYR ARG GLY GLN SEQRES 12 A 152 GLY SER PHE GLY SER SER ASP ILE TYR HET MG A 999 1 HET TRS A 153 8 HET DUP A 777 28 HET UMP A 154 20 HETNAM MG MAGNESIUM ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETSYN TRS TRIS BUFFER HETSYN UMP DUMP FORMUL 2 MG MG 2+ FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 DUP C9 H16 N3 O13 P3 FORMUL 5 UMP C9 H13 N2 O8 P FORMUL 6 HOH *131(H2 O) HELIX 1 1 SER A 29 LEU A 31 5 3 HELIX 2 2 THR A 52 GLY A 56 5 5 HELIX 3 3 ARG A 79 MET A 84 1 6 SHEET 1 A 2 GLN A 26 PRO A 27 0 SHEET 2 A 2 ILE A 64 TYR A 65 1 O TYR A 65 N GLN A 26 SHEET 1 B 4 LEU A 41 CYS A 44 0 SHEET 2 B 4 ARG A 120 PRO A 128 -1 O LEU A 124 N LEU A 41 SHEET 3 B 4 THR A 72 GLY A 78 -1 N LEU A 75 O ILE A 125 SHEET 4 B 4 GLY A 92 ILE A 94 -1 O ILE A 94 N GLY A 74 SHEET 1 C 2 THR A 49 LEU A 51 0 SHEET 2 C 2 VAL A 113 VAL A 115 -1 O VAL A 115 N THR A 49 SHEET 1 D 3 GLN A 58 LEU A 60 0 SHEET 2 D 3 ILE A 104 ALA A 108 -1 O ILE A 104 N LEU A 60 SHEET 3 D 3 LEU A 87 VAL A 89 -1 N GLN A 88 O LYS A 107 LINK OP1AUMP A 154 MG MG A 999 1555 1555 2.51 LINK O HOH A 223 MG MG A 999 1555 1555 2.16 LINK O HOH A 225 MG MG A 999 1555 1555 2.19 LINK O HOH A 245 MG MG A 999 1555 1555 1.89 LINK O2GBDUP A 777 MG MG A 999 1555 1555 2.11 LINK O1ABDUP A 777 MG MG A 999 1555 1555 2.15 LINK O1BBDUP A 777 MG MG A 999 1555 1555 2.30 CISPEP 1 GLY A 66 PRO A 67 0 8.96 SITE 1 AC1 5 UMP A 154 HOH A 223 HOH A 225 HOH A 245 SITE 2 AC1 5 DUP A 777 SITE 1 AC2 4 GLN A 88 VAL A 89 TYR A 90 PRO A 91 SITE 1 AC3 21 ILE A 76 ARG A 79 SER A 80 SER A 81 SITE 2 AC3 21 GLY A 92 VAL A 93 ILE A 94 ASP A 95 SITE 3 AC3 21 TYR A 98 GLU A 101 ILE A 102 LYS A 103 SITE 4 AC3 21 MET A 105 GLN A 123 HOH A 155 HOH A 160 SITE 5 AC3 21 HOH A 213 HOH A 223 HOH A 225 HOH A 270 SITE 6 AC3 21 MG A 999 SITE 1 AC4 15 ARG A 79 SER A 80 GLY A 92 VAL A 93 SITE 2 AC4 15 ILE A 94 ASP A 95 TYR A 98 GLU A 101 SITE 3 AC4 15 ILE A 102 LYS A 103 MET A 105 GLN A 123 SITE 4 AC4 15 HOH A 155 HOH A 160 MG A 999 CRYST1 60.559 60.559 63.635 90.00 90.00 120.00 P 63 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 0.016513 0.009534 0.000000 0.00000 SCALE2 0.000000 0.019067 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015715 0.00000