HEADER HYDROLASE 09-SEP-11 3TQ3 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 3TQ3 1 REMARK SEQADV LINK REVDAT 3 24-JAN-18 3TQ3 1 JRNL REVDAT 2 08-NOV-17 3TQ3 1 REMARK REVDAT 1 12-OCT-11 3TQ3 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 1 PMID 16582495 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10863 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 614 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 819 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 825 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -1.00000 REMARK 3 B12 (A**2) : 0.33000 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): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.208 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 919 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1270 ; 1.812 ; 2.070 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 121 ; 6.456 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 25 ;37.671 ;25.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 151 ;12.472 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;29.618 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 158 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 646 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 378 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 641 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 82 ; 0.203 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.059 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 60 ; 0.227 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.168 ; 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): 593 ; 1.115 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 952 ; 1.751 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 360 ; 2.715 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 314 ; 3.958 ; 4.500 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 25 A 137 REMARK 3 RESIDUE RANGE : A 153 A 154 REMARK 3 RESIDUE RANGE : A 777 A 777 REMARK 3 ORIGIN FOR THE GROUP (A): 2.4667 58.4802 30.3162 REMARK 3 T TENSOR REMARK 3 T11: -0.0383 T22: -0.0712 REMARK 3 T33: -0.0296 T12: 0.0035 REMARK 3 T13: -0.0079 T23: 0.0380 REMARK 3 L TENSOR REMARK 3 L11: 1.0541 L22: 1.1755 REMARK 3 L33: 2.0741 L12: 0.1926 REMARK 3 L13: -0.6254 L23: 0.2064 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: -0.0969 S13: -0.1571 REMARK 3 S21: 0.0372 S22: -0.0005 S23: -0.0088 REMARK 3 S31: 0.1085 S32: 0.1308 S33: -0.0016 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 3TQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8124 REMARK 200 MONOCHROMATOR : SI [111], HORIZONTALLY FOCUSING REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11478 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 52.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: REFMAC 5.2.0005 REMARK 200 STARTING MODEL: PDB ENTRY 2D4L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 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 32.07300 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 32.07300 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 32.07300 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: 10880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 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 60.59400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 104.95189 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -60.59400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 104.95189 REMARK 350 BIOMT3 3 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 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 24 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 117 OE1 NE2 REMARK 470 ILE A 121 CD1 REMARK 470 GLU A 131 OE1 OE2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 GLN A 137 CG CD OE1 NE2 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 N LYS A 25 O HOH A 239 2.08 REMARK 500 OG SER A 45 O HOH A 163 2.08 REMARK 500 O HOH A 234 O HOH A 250 2.08 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 ASN A 110 -5.42 -140.14 REMARK 500 VAL A 136 65.08 -102.12 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 154 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP A 153 O1A REMARK 620 2 DUP A 153 O2G 86.8 REMARK 620 3 DUP A 153 O1B 88.6 87.0 REMARK 620 4 HOH A 226 O 96.0 84.2 169.9 REMARK 620 5 HOH A 230 O 176.0 91.1 87.9 87.2 REMARK 620 6 UMP A 777 OP1 26.8 80.5 62.4 120.8 149.3 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 UMP A 777 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG 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: 3TPY 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 3TQ3 A 1 152 UNP O92810 O92810_MPMV 608 759 SEQADV 3TQ3 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 UMP A 777 20 HET DUP A 153 28 HET MG A 154 1 HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN UMP DUMP FORMUL 2 UMP C9 H13 N2 O8 P FORMUL 3 DUP C9 H16 N3 O13 P3 FORMUL 4 MG MG 2+ FORMUL 5 HOH *99(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 LYS A 85 1 7 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 LEU A 77 -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 O1ABDUP A 153 MG MG A 154 1555 1555 1.93 LINK O2GBDUP A 153 MG MG A 154 1555 1555 2.01 LINK O1BBDUP A 153 MG MG A 154 1555 1555 2.12 LINK MG MG A 154 O HOH A 226 1555 1555 2.17 LINK MG MG A 154 O HOH A 230 1555 1555 2.15 LINK MG MG A 154 OP1AUMP A 777 1555 1555 2.52 CISPEP 1 GLY A 66 PRO A 67 0 9.34 SITE 1 AC1 16 ILE A 76 ARG A 79 SER A 80 GLY A 92 SITE 2 AC1 16 VAL A 93 ILE A 94 ASP A 95 TYR A 98 SITE 3 AC1 16 GLU A 101 ILE A 102 LYS A 103 MET A 105 SITE 4 AC1 16 GLN A 123 MG A 154 HOH A 155 HOH A 158 SITE 1 AC2 23 ILE A 76 ARG A 79 SER A 80 SER A 81 SITE 2 AC2 23 GLY A 92 VAL A 93 ILE A 94 ASP A 95 SITE 3 AC2 23 TYR A 98 GLU A 101 ILE A 102 LYS A 103 SITE 4 AC2 23 MET A 105 GLN A 123 MG A 154 HOH A 155 SITE 5 AC2 23 HOH A 158 HOH A 226 HOH A 230 HOH A 235 SITE 6 AC2 23 HOH A 245 HOH A 246 HOH A 247 SITE 1 AC3 5 DUP A 153 HOH A 226 HOH A 230 HOH A 235 SITE 2 AC3 5 UMP A 777 CRYST1 60.594 60.594 64.146 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 0.016503 0.009528 0.000000 0.00000 SCALE2 0.000000 0.019056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015589 0.00000