PDB Short entry for 3ER9 HEADER TRANSCRIPTION, TRANSFERASE/RNA 01-OCT-08 3ER9 TITLE CRYSTAL STRUCTURE OF THE HETERODIMERIC VACCINIA VIRUS MRNA TITLE 2 POLYADENYLATE POLYMERASE COMPLEX WITH UU AND 3'-DEOXY ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAP-SPECIFIC MRNA (NUCLEOSIDE-2'-O-)-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLY(A) POLYMERASE REGULATORY SUBUNIT, POLY(A) POLYMERASE COMPND 5 SMALL SUBUNIT, PAP-S, VP39; COMPND 6 EC: 2.1.1.57; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: POLY(A) POLYMERASE CATALYTIC SUBUNIT; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: POLY(A) POLYMERASE LARGE SUBUNIT, PAP-L, VP55; COMPND 13 EC: 2.7.7.19; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: 5'-R(UP*U)-3'; COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS WR; SOURCE 3 ORGANISM_TAXID: 10254; SOURCE 4 STRAIN: WESTERN RESERVE / WR; SOURCE 5 GENE: PAPS, VACWR095, F9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: VACCINIA VIRUS WR; SOURCE 13 ORGANISM_TAXID: 10254; SOURCE 14 STRAIN: WESTERN RESERVE / WR; SOURCE 15 GENE: PAPL, VACWR057, E1L; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES KEYWDS POLYADENYLATE POLYMERASE, TRANSLOCATION, SINGLE TRANDED RNA POLY(A) KEYWDS 2 POLYMERASE, RNA PROTEIN COMPLEX, PROCESSIVITY, HETERODIMER, KEYWDS 3 NUCLEOTIDYLTRANSFERASE, POXVIRUS; METHYLTRANSFERASE, MRNA CAPPING, KEYWDS 4 MRNA PROCESSING, S-ADENOSYL-L-METHIONINE, TRANSCRIPTION, KEYWDS 5 TRANSFERASE, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.LI,H.LI,S.ZHOU,T.L.POULOS,P.D.GERSHON REVDAT 5 27-DEC-23 3ER9 1 REMARK REVDAT 4 20-OCT-21 3ER9 1 REMARK SEQADV LINK REVDAT 3 24-JAN-18 3ER9 1 AUTHOR REVDAT 2 13-JUL-11 3ER9 1 VERSN REVDAT 1 16-JUN-09 3ER9 0 JRNL AUTH C.LI,H.LI,S.ZHOU,E.SUN,J.YOSHIZAWA,T.L.POULOS,P.D.GERSHON JRNL TITL POLYMERASE TRANSLOCATION WITH RESPECT TO SINGLE-STRANDED JRNL TITL 2 NUCLEIC ACID: LOOPING OR WRAPPING OF PRIMER AROUND A POLY(A) JRNL TITL 3 POLYMERASE JRNL REF STRUCTURE V. 17 680 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19446524 JRNL DOI 10.1016/J.STR.2009.03.012 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.M.MOURE,B.R.BOWMAN,P.D.GERSHON,F.A.QUIOCHO REMARK 1 TITL CRYSTAL STRUCTURE OF THE VACCINIA VIRUS POLYADENYLATE REMARK 1 TITL 2 POLYMERASE HETERODIMER: INSIGHT INTO ATP SELECTTIVITY AND REMARK 1 TITL 3 PROCESSIVITY REMARK 1 REF MOL.CELL V. 22 339 2006 REMARK 1 REFN ISSN 1097-2765 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1705112.390 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 52739 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 SET) : 0.208 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2660 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8068 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 446 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6009 REMARK 3 NUCLEIC ACID ATOMS : 40 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 317 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.42000 REMARK 3 B22 (A**2) : 2.87000 REMARK 3 B33 (A**2) : -5.29000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.16 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.360 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.110 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL, BULK FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 56.83 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA1.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : 3ATP.PAR REMARK 3 PARAMETER FILE 5 : GOL.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : &_1_TOPOLOGY_INFILE_1 REMARK 3 TOPOLOGY FILE 2 : &_1_TOPOLOGY_INFILE_2 REMARK 3 TOPOLOGY FILE 3 : &_1_TOPOLOGY_INFILE_3 REMARK 3 TOPOLOGY FILE 4 : &_1_TOPOLOGY_INFILE_4 REMARK 3 TOPOLOGY FILE 5 : &_1_TOPOLOGY_INFILE_5 REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 27-32, 142-144 IN CHAINS A AND REMARK 3 RESIDUES 1-11, 118-129, 150-160 IN CHAINS B ARE DISORDERED AND REMARK 3 NOT INCLUDED IN THE MODEL. REMARK 4 REMARK 4 3ER9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000049671. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 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 : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52976 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.53000 REMARK 200 R SYM (I) : 0.53000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : 0.37100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEINS(4-5MG.ML) IN 10MM TRIS-HCL, REMARK 280 PH 8.7, 75 MM NACL, 0.5 MM DTT, MIXED WITH EQUAL VOLUME BUFFER REMARK 280 WHICH COMPOSED OF 10MM TRIS-HCL, PH 8.7, 15-20% PEG 4000, 5% REMARK 280 GLYCEROL, 0.5 MM DTT. ROOM TEMPERATURE FOR SEVERAL DAYS., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 34.76550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.86700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.98850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.86700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.76550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.98850 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D 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 27 REMARK 465 ASN A 28 REMARK 465 GLU A 29 REMARK 465 VAL A 30 REMARK 465 ALA A 31 REMARK 465 LYS A 32 REMARK 465 ALA A 142 REMARK 465 ALA A 143 REMARK 465 GLY A 144 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ARG B 3 REMARK 465 ASN B 4 REMARK 465 PRO B 5 REMARK 465 ASP B 6 REMARK 465 GLN B 7 REMARK 465 ASN B 8 REMARK 465 THR B 9 REMARK 465 LEU B 10 REMARK 465 PRO B 11 REMARK 465 LYS B 118 REMARK 465 ALA B 119 REMARK 465 PRO B 120 REMARK 465 ASN B 121 REMARK 465 VAL B 122 REMARK 465 ILE B 123 REMARK 465 SER B 124 REMARK 465 SER B 125 REMARK 465 LYS B 126 REMARK 465 ILE B 127 REMARK 465 SER B 128 REMARK 465 TYR B 129 REMARK 465 ILE B 150 REMARK 465 ASP B 151 REMARK 465 LYS B 152 REMARK 465 ALA B 153 REMARK 465 LYS B 154 REMARK 465 VAL B 155 REMARK 465 MET B 156 REMARK 465 GLY B 157 REMARK 465 ARG B 158 REMARK 465 HIS B 159 REMARK 465 ASN B 160 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 114 146.10 -175.73 REMARK 500 ASN A 146 106.98 49.45 REMARK 500 GLU A 147 88.54 57.05 REMARK 500 GLU A 217 55.60 -104.97 REMARK 500 ILE A 242 -64.62 -95.71 REMARK 500 ASN B 329 -133.45 66.10 REMARK 500 GLU B 382 -136.99 53.24 REMARK 500 SER B 387 157.74 179.58 REMARK 500 TYR B 435 -22.18 -157.40 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 CA B 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 202 OD1 REMARK 620 2 ASP B 204 OD1 77.5 REMARK 620 3 ASP B 204 OD2 110.3 53.3 REMARK 620 4 3AT B 800 O3G 81.8 154.3 150.9 REMARK 620 5 3AT B 800 O1B 138.9 134.0 83.1 71.5 REMARK 620 6 3AT B 800 O1A 143.2 100.7 96.5 86.7 66.9 REMARK 620 7 HOH B1066 O 67.4 101.4 76.8 84.4 79.1 146.0 REMARK 620 8 HOH B1310 O 73.7 74.1 122.9 85.6 132.3 70.6 140.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 202 OD2 REMARK 620 2 ASP B 204 OD1 86.1 REMARK 620 3 HOH B1308 O 142.9 83.4 REMARK 620 4 HOH B1310 O 64.9 78.5 78.1 REMARK 620 5 HOH B1311 O 161.0 95.1 55.8 133.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3AT B 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 880 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 890 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GA9 RELATED DB: PDB REMARK 900 HETERODIMER STRUCTURE WITH BOUND ATP ANALOGS REMARK 900 RELATED ID: 3ER8 RELATED DB: PDB REMARK 900 RELATED ID: 3ERC RELATED DB: PDB DBREF 3ER9 A 1 297 UNP P07617 PAP2_VACCV 1 297 DBREF 3ER9 B 1 479 UNP P23371 PAP1_VACCV 1 479 DBREF 3ER9 D 600 601 PDB 3ER9 3ER9 600 601 SEQADV 3ER9 ALA A 140 UNP P07617 ARG 140 ENGINEERED MUTATION SEQADV 3ER9 ALA A 142 UNP P07617 LYS 142 ENGINEERED MUTATION SEQADV 3ER9 ALA A 143 UNP P07617 ARG 143 ENGINEERED MUTATION SEQADV 3ER9 SER B 36 UNP P23371 LEU 36 ENGINEERED MUTATION SEQRES 1 A 297 MET ASP VAL VAL SER LEU ASP LYS PRO PHE MET TYR PHE SEQRES 2 A 297 GLU GLU ILE ASP ASN GLU LEU ASP TYR GLU PRO GLU SER SEQRES 3 A 297 ALA ASN GLU VAL ALA LYS LYS LEU PRO TYR GLN GLY GLN SEQRES 4 A 297 LEU LYS LEU LEU LEU GLY GLU LEU PHE PHE LEU SER LYS SEQRES 5 A 297 LEU GLN ARG HIS GLY ILE LEU ASP GLY ALA THR VAL VAL SEQRES 6 A 297 TYR ILE GLY SER ALA PRO GLY THR HIS ILE ARG TYR LEU SEQRES 7 A 297 ARG ASP HIS PHE TYR ASN LEU GLY VAL ILE ILE LYS TRP SEQRES 8 A 297 MET LEU ILE ASP GLY ARG HIS HIS ASP PRO ILE LEU ASN SEQRES 9 A 297 GLY LEU ARG ASP VAL THR LEU VAL THR ARG PHE VAL ASP SEQRES 10 A 297 GLU GLU TYR LEU ARG SER ILE LYS LYS GLN LEU HIS PRO SEQRES 11 A 297 SER LYS ILE ILE LEU ILE SER ASP VAL ALA SER ALA ALA SEQRES 12 A 297 GLY GLY ASN GLU PRO SER THR ALA ASP LEU LEU SER ASN SEQRES 13 A 297 TYR ALA LEU GLN ASN VAL MET ILE SER ILE LEU ASN PRO SEQRES 14 A 297 VAL ALA SER SER LEU LYS TRP ARG CYS PRO PHE PRO ASP SEQRES 15 A 297 GLN TRP ILE LYS ASP PHE TYR ILE PRO HIS GLY ASN LYS SEQRES 16 A 297 MET LEU GLN PRO PHE ALA PRO SER TYR SER ALA GLU MET SEQRES 17 A 297 ARG LEU LEU SER ILE TYR THR GLY GLU ASN MET ARG LEU SEQRES 18 A 297 THR ARG VAL THR LYS SER ASP ALA VAL ASN TYR GLU LYS SEQRES 19 A 297 LYS MET TYR TYR LEU ASN LYS ILE VAL ARG ASN LYS VAL SEQRES 20 A 297 VAL VAL ASN PHE ASP TYR PRO ASN GLN GLU TYR ASP TYR SEQRES 21 A 297 PHE HIS MET TYR PHE MET LEU ARG THR VAL TYR CYS ASN SEQRES 22 A 297 LYS THR PHE PRO THR THR LYS ALA LYS VAL LEU PHE LEU SEQRES 23 A 297 GLN GLN SER ILE PHE ARG PHE LEU ASN ILE PRO SEQRES 1 B 479 MET ASN ARG ASN PRO ASP GLN ASN THR LEU PRO ASN ILE SEQRES 2 B 479 THR LEU LYS ILE ILE GLU THR TYR LEU GLY ARG VAL PRO SEQRES 3 B 479 SER VAL ASN GLU TYR HIS MET LEU LYS SER GLN ALA ARG SEQRES 4 B 479 ASN ILE GLN LYS ILE THR VAL PHE ASN LYS ASP ILE PHE SEQRES 5 B 479 VAL SER LEU VAL LYS LYS ASN LYS LYS ARG PHE PHE SER SEQRES 6 B 479 ASP VAL ASN THR SER ALA SER GLU ILE LYS ASP ARG ILE SEQRES 7 B 479 LEU SER TYR PHE SER LYS GLN THR GLN THR TYR ASN ILE SEQRES 8 B 479 GLY LYS LEU PHE THR ILE ILE GLU LEU GLN SER VAL LEU SEQRES 9 B 479 VAL THR THR TYR THR ASP ILE LEU GLY VAL LEU THR ILE SEQRES 10 B 479 LYS ALA PRO ASN VAL ILE SER SER LYS ILE SER TYR ASN SEQRES 11 B 479 VAL THR SER MET GLU GLU LEU ALA ARG ASP MET LEU ASN SEQRES 12 B 479 SER MET ASN VAL ALA VAL ILE ASP LYS ALA LYS VAL MET SEQRES 13 B 479 GLY ARG HIS ASN VAL SER SER LEU VAL LYS ASN VAL ASN SEQRES 14 B 479 LYS LEU MET GLU GLU TYR LEU ARG ARG HIS ASN LYS SER SEQRES 15 B 479 CYS ILE CYS TYR GLY SER TYR SER LEU TYR LEU ILE ASN SEQRES 16 B 479 PRO ASN ILE ARG TYR GLY ASP ILE ASP ILE LEU GLN THR SEQRES 17 B 479 ASN SER ARG THR PHE LEU ILE ASP LEU ALA PHE LEU ILE SEQRES 18 B 479 LYS PHE ILE THR GLY ASN ASN ILE ILE LEU SER LYS ILE SEQRES 19 B 479 PRO TYR LEU ARG ASN TYR MET VAL ILE LYS ASP GLU ASN SEQRES 20 B 479 ASP ASN HIS ILE ILE ASP SER PHE ASN ILE ARG GLN ASP SEQRES 21 B 479 THR MET ASN VAL VAL PRO LYS ILE PHE ILE ASP ASN ILE SEQRES 22 B 479 TYR ILE VAL ASP PRO THR PHE GLN LEU LEU ASN MET ILE SEQRES 23 B 479 LYS MET PHE SER GLN ILE ASP ARG LEU GLU ASP LEU SER SEQRES 24 B 479 LYS ASP PRO GLU LYS PHE ASN ALA ARG MET ALA THR MET SEQRES 25 B 479 LEU GLU TYR VAL ARG TYR THR HIS GLY ILE VAL PHE ASP SEQRES 26 B 479 GLY LYS ARG ASN ASN MET PRO MET LYS CYS ILE ILE ASP SEQRES 27 B 479 GLU ASN ASN ARG ILE VAL THR VAL THR THR LYS ASP TYR SEQRES 28 B 479 PHE SER PHE LYS LYS CYS LEU VAL TYR LEU ASP GLU ASN SEQRES 29 B 479 VAL LEU SER SER ASP ILE LEU ASP LEU ASN ALA ASP THR SEQRES 30 B 479 SER CYS ASP PHE GLU SER VAL THR ASN SER VAL TYR LEU SEQRES 31 B 479 ILE HIS ASP ASN ILE MET TYR THR TYR PHE SER ASN THR SEQRES 32 B 479 ILE LEU LEU SER ASP LYS GLY LYS VAL HIS GLU ILE SER SEQRES 33 B 479 ALA ARG GLY LEU CYS ALA HIS ILE LEU LEU TYR GLN MET SEQRES 34 B 479 LEU THR SER GLY GLU TYR LYS GLN CYS LEU SER ASP LEU SEQRES 35 B 479 LEU ASN SER MET MET ASN ARG ASP LYS ILE PRO ILE TYR SEQRES 36 B 479 SER HIS THR GLU ARG ASP LYS LYS PRO GLY ARG HIS GLY SEQRES 37 B 479 PHE ILE ASN ILE GLU LYS ASP ILE ILE VAL PHE SEQRES 1 D 2 U U HET GOL A 880 6 HET GOL A 890 6 HET GOL A 900 6 HET 3AT B 800 30 HET CA B 901 1 HET CA B 902 1 HETNAM GOL GLYCEROL HETNAM 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 3AT CORDYCEPIN TRIPHOSPHATE FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 3AT C10 H16 N5 O12 P3 FORMUL 8 CA 2(CA 2+) FORMUL 10 HOH *317(H2 O) HELIX 1 1 TYR A 12 ILE A 16 5 5 HELIX 2 2 TYR A 36 HIS A 56 1 21 HELIX 3 3 GLY A 72 LEU A 85 1 14 HELIX 4 4 ASP A 100 ASN A 104 5 5 HELIX 5 5 ASP A 117 HIS A 129 1 13 HELIX 6 6 SER A 149 ASN A 168 1 20 HELIX 7 7 PHE A 180 TRP A 184 5 5 HELIX 8 8 THR A 225 ILE A 242 1 18 HELIX 9 9 VAL A 243 LYS A 246 5 4 HELIX 10 10 GLU A 257 ARG A 268 1 12 HELIX 11 11 THR A 278 ASN A 295 1 18 HELIX 12 12 ASN B 12 GLY B 23 1 12 HELIX 13 13 SER B 27 LYS B 35 1 9 HELIX 14 14 GLN B 37 PHE B 47 1 11 HELIX 15 15 ASN B 48 PHE B 64 1 17 HELIX 16 16 SER B 70 PHE B 82 1 13 HELIX 17 17 SER B 83 THR B 88 5 6 HELIX 18 18 ASN B 90 LEU B 112 1 23 HELIX 19 19 GLY B 113 ILE B 117 5 5 HELIX 20 20 ASN B 130 SER B 133 5 4 HELIX 21 21 MET B 134 ASN B 146 1 13 HELIX 22 22 LEU B 164 HIS B 179 1 16 HELIX 23 23 GLY B 187 LEU B 193 1 7 HELIX 24 24 ASN B 209 GLY B 226 1 18 HELIX 25 25 ARG B 258 VAL B 265 1 8 HELIX 26 26 ASP B 277 PHE B 289 1 13 HELIX 27 27 GLN B 291 ASP B 301 1 11 HELIX 28 28 ASP B 301 GLY B 321 1 21 HELIX 29 29 ASP B 362 LEU B 373 1 12 HELIX 30 30 GLU B 382 THR B 385 5 4 HELIX 31 31 HIS B 413 THR B 431 1 19 HELIX 32 32 TYR B 435 SER B 445 1 11 SHEET 1 A 2 VAL A 3 VAL A 4 0 SHEET 2 A 2 VAL A 247 VAL A 248 1 O VAL A 247 N VAL A 4 SHEET 1 B 7 VAL A 109 THR A 113 0 SHEET 2 B 7 LYS A 90 ASP A 95 1 N LEU A 93 O VAL A 112 SHEET 3 B 7 THR A 63 ILE A 67 1 N TYR A 66 O ILE A 94 SHEET 4 B 7 ILE A 133 SER A 137 1 O ILE A 134 N VAL A 65 SHEET 5 B 7 ALA A 171 TRP A 176 1 O SER A 173 N SER A 137 SHEET 6 B 7 MET A 208 ILE A 213 -1 O MET A 208 N TRP A 176 SHEET 7 B 7 ASN A 194 MET A 196 -1 N ASN A 194 O LEU A 211 SHEET 1 C 2 PHE A 188 ILE A 190 0 SHEET 2 C 2 THR A 222 VAL A 224 -1 O THR A 222 N ILE A 190 SHEET 1 D 7 CYS B 183 TYR B 186 0 SHEET 2 D 7 ASP B 204 GLN B 207 -1 O LEU B 206 N ILE B 184 SHEET 3 D 7 HIS B 250 ASN B 256 1 O PHE B 255 N GLN B 207 SHEET 4 D 7 TYR B 240 LYS B 244 -1 N ILE B 243 O ILE B 252 SHEET 5 D 7 ILE B 230 LYS B 233 -1 N ILE B 230 O LYS B 244 SHEET 6 D 7 GLY B 468 ASN B 471 -1 O ILE B 470 N LEU B 231 SHEET 7 D 7 ILE B 476 VAL B 478 -1 O ILE B 476 N ASN B 471 SHEET 1 E 2 LYS B 267 ILE B 270 0 SHEET 2 E 2 ILE B 273 VAL B 276 -1 O ILE B 273 N ILE B 270 SHEET 1 F 6 CYS B 335 ASP B 338 0 SHEET 2 F 6 ILE B 343 THR B 347 -1 O THR B 345 N ILE B 336 SHEET 3 F 6 LYS B 356 TYR B 360 -1 O VAL B 359 N VAL B 344 SHEET 4 F 6 ILE B 395 TYR B 399 1 O MET B 396 N LEU B 358 SHEET 5 F 6 VAL B 388 HIS B 392 -1 N LEU B 390 O TYR B 397 SHEET 6 F 6 CYS B 379 ASP B 380 -1 N CYS B 379 O TYR B 389 SHEET 1 G 3 LYS B 411 VAL B 412 0 SHEET 2 G 3 LEU B 405 ASP B 408 -1 N ASP B 408 O LYS B 411 SHEET 3 G 3 SER B 456 HIS B 457 -1 O SER B 456 N LEU B 406 LINK OD1 ASP B 202 CA CA B 901 1555 1555 2.40 LINK OD2 ASP B 202 CA CA B 902 1555 1555 2.42 LINK OD1 ASP B 204 CA CA B 901 1555 1555 2.43 LINK OD2 ASP B 204 CA CA B 901 1555 1555 2.43 LINK OD1 ASP B 204 CA CA B 902 1555 1555 2.40 LINK O3G 3AT B 800 CA CA B 901 1555 1555 2.39 LINK O1B 3AT B 800 CA CA B 901 1555 1555 2.40 LINK O1A 3AT B 800 CA CA B 901 1555 1555 2.34 LINK CA CA B 901 O HOH B1066 1555 1555 2.40 LINK CA CA B 901 O HOH B1310 1555 1555 2.62 LINK CA CA B 902 O HOH B1308 1555 1555 2.72 LINK CA CA B 902 O HOH B1310 1555 1555 2.41 LINK CA CA B 902 O HOH B1311 1555 1555 2.41 CISPEP 1 ALA A 70 PRO A 71 0 0.06 CISPEP 2 HIS A 129 PRO A 130 0 0.16 CISPEP 3 MET B 331 PRO B 332 0 -0.31 SITE 1 AC1 18 SER B 188 GLY B 201 ASP B 202 ASP B 204 SITE 2 AC1 18 GLN B 281 ASN B 284 MET B 288 ARG B 294 SITE 3 AC1 18 LYS B 304 ARG B 308 ASN B 402 CA B 901 SITE 4 AC1 18 HOH B1066 HOH B1210 HOH B1235 HOH B1250 SITE 5 AC1 18 HOH B1298 HOH B1310 SITE 1 AC2 5 ASP B 202 ASP B 204 3AT B 800 HOH B1066 SITE 2 AC2 5 HOH B1310 SITE 1 AC3 5 ASP B 202 ASP B 204 HOH B1308 HOH B1310 SITE 2 AC3 5 HOH B1311 SITE 1 AC4 5 PHE A 251 ASP A 252 TYR A 264 HOH A1085 SITE 2 AC4 5 HOH A1306 SITE 1 AC5 5 TYR A 77 HIS A 81 ASN A 84 HOH A1204 SITE 2 AC5 5 HOH A1303 SITE 1 AC6 1 THR A 279 CRYST1 69.531 91.977 133.734 90.00 90.00 90.00 P 21 21 21 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 0.014382 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007478 0.00000