HEADER HYDROLASE 20-OCT-05 2D4N TITLE CRYSTAL STRUCTURE OF M-PMV DUTPASE COMPLEXED WITH DUPNPP, SUBSTRATE TITLE 2 ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 83-234; COMPND 5 SYNONYM: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE; COMPND 6 EC: 3.6.1.23; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MASON-PFIZER MONKEY VIRUS; SOURCE 3 ORGANISM_TAXID: 11855; SOURCE 4 GENE: GAG-PRO; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS JELLY ROLL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.NEMETH,O.BARABAS,G.B.VERTESSY REVDAT 7 25-OCT-23 2D4N 1 REMARK REVDAT 6 10-NOV-21 2D4N 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 2D4N 1 REMARK REVDAT 4 20-JUL-11 2D4N 1 JRNL REVDAT 3 13-JUL-11 2D4N 1 VERSN REVDAT 2 24-FEB-09 2D4N 1 VERSN REVDAT 1 21-NOV-06 2D4N 0 JRNL AUTH V.NEMETH-PONGRACZ,O.BARABAS,M.FUXREITER,I.SIMON,I.PICHOVA, JRNL AUTH 2 M.RUMLOVA,H.ZABRANSKA,D.SVERGUN,M.PETOUKHOV,V.HARMAT, JRNL AUTH 3 E.KLEMENT,E.HUNYADI-GULYAS,K.F.MEDZIHRADSZKY,E.KONYA, JRNL AUTH 4 B.G.VERTESSY JRNL TITL FLEXIBLE SEGMENTS MODULATE CO-FOLDING OF DUTPASE AND JRNL TITL 2 NUCLEOCAPSID PROTEINS. JRNL REF NUCLEIC ACIDS RES. V. 35 495 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17169987 JRNL DOI 10.1093/NAR/GKL1074 REMARK 2 REMARK 2 RESOLUTION. 1.53 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 19296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : FROM STARTING MODEL REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1097 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1409 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : 0.61000 REMARK 3 B33 (A**2) : -0.91000 REMARK 3 B12 (A**2) : 0.30000 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): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 910 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1255 ; 1.911 ; 2.050 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 124 ; 5.752 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 26 ;36.353 ;25.769 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 153 ;11.110 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;30.573 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 154 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 645 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 395 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 637 ; 0.315 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 100 ; 0.218 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.002 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 76 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.172 ; 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): 596 ; 2.624 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 964 ; 3.883 ;10.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 341 ; 8.097 ;50.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 286 ;10.457 ;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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 107 A 219 REMARK 3 ORIGIN FOR THE GROUP (A): 2.4987 59.1533 30.6610 REMARK 3 T TENSOR REMARK 3 T11: -0.0165 T22: -0.0444 REMARK 3 T33: -0.0041 T12: 0.0045 REMARK 3 T13: -0.0033 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.4966 L22: 0.6739 REMARK 3 L33: 1.0476 L12: -0.0433 REMARK 3 L13: -0.0637 L23: 0.1368 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: -0.0240 S13: -0.0736 REMARK 3 S21: -0.0111 S22: 0.0310 S23: -0.0199 REMARK 3 S31: 0.0919 S32: 0.0691 S33: -0.0377 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, RIGID BODY REFINEMENT REMARK 4 REMARK 4 2D4N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000024981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-04 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) : 0.8128 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20787 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 52.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 2.660 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.05700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.13 REMARK 200 R MERGE FOR SHELL (I) : 0.44200 REMARK 200 R SYM FOR SHELL (I) : 0.33400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2D4L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM CHLORIDE, TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K 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 32.17850 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 32.17850 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 32.17850 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TRIMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: 2-Y,2+X-Y,Z AND - REMARK 300 X+Y,2-X,Z 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 61.07100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 105.77807 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -61.07100 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 105.77807 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 C TRS A1001 LIES ON A SPECIAL POSITION. REMARK 375 N TRS A1001 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 83 REMARK 465 ARG A 84 REMARK 465 VAL A 85 REMARK 465 GLU A 86 REMARK 465 GLY A 87 REMARK 465 PRO A 88 REMARK 465 ALA A 89 REMARK 465 PRO A 90 REMARK 465 GLY A 91 REMARK 465 PRO A 92 REMARK 465 GLU A 93 REMARK 465 THR A 94 REMARK 465 SER A 95 REMARK 465 LEU A 96 REMARK 465 TRP A 97 REMARK 465 GLY A 98 REMARK 465 SER A 99 REMARK 465 GLN A 100 REMARK 465 LEU A 101 REMARK 465 CYS A 102 REMARK 465 SER A 103 REMARK 465 SER A 104 REMARK 465 GLN A 105 REMARK 465 GLN A 106 REMARK 465 GLN A 220 REMARK 465 PRO A 221 REMARK 465 TYR A 222 REMARK 465 ARG A 223 REMARK 465 GLY A 224 REMARK 465 GLN A 225 REMARK 465 GLY A 226 REMARK 465 SER A 227 REMARK 465 PHE A 228 REMARK 465 GLY A 229 REMARK 465 SER A 230 REMARK 465 SER A 231 REMARK 465 ASP A 232 REMARK 465 ILE A 233 REMARK 465 TYR A 234 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 LYS A 167 CD CE NZ REMARK 470 VAL A 197 CB CG1 CG2 REMARK 470 ILE A 203 CD1 REMARK 470 LYS A 217 CE NZ REMARK 470 GLN A 219 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 OG SER A 127 O HOH A 1115 1.76 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 DUP A 777 O2G REMARK 620 2 DUP A 777 O1B 92.2 REMARK 620 3 DUP A 777 O1A 96.0 88.7 REMARK 620 4 HOH A1127 O 89.5 87.4 173.4 REMARK 620 5 HOH A1128 O 173.2 93.7 87.6 87.3 REMARK 620 6 HOH A1130 O 87.3 178.2 89.7 94.3 87.0 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 MG A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 777 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AKV RELATED DB: PDB REMARK 900 THE FULL LENGTH PROTEIN COMPLEXED WITH REACTION INTERMEDIATE REMARK 900 RELATED ID: 2D4L RELATED DB: PDB REMARK 900 THE FULL LENGTH PROTEIN, APO REMARK 900 RELATED ID: 2D4M RELATED DB: PDB REMARK 900 THE FULL LENGTH PROTEIN, APO DBREF 2D4N A 83 234 GB 40018527 NP_954564 83 234 SEQADV 2D4N LYS A 83 GB 40018527 ASN 83 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 DUP A 777 28 HET TRS A1001 8 HETNAM MG MAGNESIUM ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 MG MG 2+ FORMUL 3 DUP C9 H16 N3 O13 P3 FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 HOH *137(H2 O) HELIX 1 1 SER A 111 LEU A 113 5 3 HELIX 2 2 THR A 134 GLY A 138 5 5 HELIX 3 3 ARG A 161 LYS A 167 1 7 SHEET 1 A 4 GLN A 108 PRO A 109 0 SHEET 2 A 4 GLN A 140 TYR A 147 1 O TYR A 147 N GLN A 108 SHEET 3 A 4 GLU A 183 ALA A 190 -1 O ILE A 184 N ILE A 146 SHEET 4 A 4 LEU A 169 VAL A 171 -1 N GLN A 170 O LYS A 189 SHEET 1 B 4 LEU A 123 CYS A 126 0 SHEET 2 B 4 ARG A 202 PRO A 210 -1 O ALA A 204 N LEU A 125 SHEET 3 B 4 THR A 154 LEU A 159 -1 N LEU A 157 O ILE A 207 SHEET 4 B 4 GLY A 174 ILE A 176 -1 O GLY A 174 N ILE A 158 SHEET 1 C 2 THR A 131 LEU A 133 0 SHEET 2 C 2 VAL A 195 VAL A 197 -1 O VAL A 197 N THR A 131 LINK O2G DUP A 777 MG MG A 999 1555 1555 1.99 LINK O1B DUP A 777 MG MG A 999 1555 1555 2.05 LINK O1A DUP A 777 MG MG A 999 1555 1555 2.09 LINK MG MG A 999 O HOH A1127 1555 1555 2.04 LINK MG MG A 999 O HOH A1128 1555 1555 2.12 LINK MG MG A 999 O HOH A1130 1555 1555 2.12 CISPEP 1 GLY A 148 PRO A 149 0 10.87 SITE 1 AC1 4 DUP A 777 HOH A1127 HOH A1128 HOH A1130 SITE 1 AC2 23 ARG A 161 SER A 162 SER A 163 GLY A 174 SITE 2 AC2 23 VAL A 175 ILE A 176 ASP A 177 TYR A 180 SITE 3 AC2 23 GLU A 183 ILE A 184 LYS A 185 MET A 187 SITE 4 AC2 23 GLN A 205 MG A 999 HOH A1002 HOH A1010 SITE 5 AC2 23 HOH A1013 HOH A1077 HOH A1103 HOH A1127 SITE 6 AC2 23 HOH A1128 HOH A1130 HOH A1131 SITE 1 AC3 4 GLN A 170 VAL A 171 TYR A 172 PRO A 173 CRYST1 61.071 61.071 64.357 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 0.016374 0.009454 0.000000 0.00000 SCALE2 0.000000 0.018908 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015538 0.00000