HEADER TRANSFERASE 20-AUG-01 1JTE TITLE CRYSTAL STRUCTURE ANALYSIS OF VP39 F180W MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: VP39; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-307; COMPND 5 SYNONYM: POLY(A) POLYMERASE REGULATORY SUBUNIT; COMPND 6 EC: 2.7.7.19; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS; SOURCE 3 ORGANISM_TAXID: 10245; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PPG177 KEYWDS VP39, MRNA CAP-BINDING PROTEIN, METHYLTRANSFERASE, MUTANT, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.HU,A.OGURO,P.D.GERSHON,F.A.QUIOCHO REVDAT 5 29-MAY-24 1JTE 1 REMARK REVDAT 4 10-NOV-21 1JTE 1 REMARK SEQADV REVDAT 3 24-FEB-09 1JTE 1 VERSN REVDAT 2 18-DEC-02 1JTE 1 REMARK REVDAT 1 10-JUL-02 1JTE 0 JRNL AUTH G.HU,A.OGURO,C.LI,P.D.GERSHON,F.A.QUIOCHO JRNL TITL THE "CAP-BINDING SLOT" OF AN MRNA CAP-BINDING PROTEIN: JRNL TITL 2 QUANTITATIVE EFFECTS OF AROMATIC SIDE CHAIN CHOICE IN THE JRNL TITL 3 DOUBLE-STACKING SANDWICH WITH CAP. JRNL REF BIOCHEMISTRY V. 41 7677 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12056899 JRNL DOI 10.1021/BI0201926 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 23043 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.958 REMARK 3 FREE R VALUE TEST SET COUNT : 2525 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 68 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2405 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.630 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.43 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.450 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JTE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT (SIEMENS) REMARK 200 DATA SCALING SOFTWARE : SAINT (SIEMENS) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23570 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, SODIUM CITRATE, AMMONIUM REMARK 280 SULPHATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.32000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.32000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.97000 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: MONOMERIC 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 LYS A 142 REMARK 465 ARG A 143 REMARK 465 GLY A 144 REMARK 465 GLY A 145 REMARK 465 ASN A 146 REMARK 465 GLU A 147 REMARK 465 THR A 298 REMARK 465 THR A 299 REMARK 465 SER A 300 REMARK 465 THR A 301 REMARK 465 GLU A 302 REMARK 465 LYS A 303 REMARK 465 VAL A 304 REMARK 465 SER A 305 REMARK 465 HIS A 306 REMARK 465 GLU A 307 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 ARG A 140 CG CD NE CZ NH1 NH2 REMARK 470 SER A 141 OG 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 PRO A 101 -9.35 -54.57 REMARK 500 ASP A 138 31.26 -144.00 REMARK 500 ILE A 185 -59.29 -120.47 REMARK 500 ILE A 242 -66.98 -96.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JSZ RELATED DB: PDB REMARK 900 1JSZ CONTAINS THE SAME PROTEIN COMPLEXED WITH N7,9-DIMETHYLGUANINE REMARK 900 RELATED ID: 1JTF RELATED DB: PDB REMARK 900 1JTF CONTAINS THE SAME PROTEIN COMPLEXED WITH M7GPPPG DBREF 1JTE A 1 307 UNP P07617 PAP2_VACCV 1 307 SEQADV 1JTE TRP A 180 UNP P07617 PHE 180 ENGINEERED MUTATION SEQRES 1 A 307 MET ASP VAL VAL SER LEU ASP LYS PRO PHE MET TYR PHE SEQRES 2 A 307 GLU GLU ILE ASP ASN GLU LEU ASP TYR GLU PRO GLU SER SEQRES 3 A 307 ALA ASN GLU VAL ALA LYS LYS LEU PRO TYR GLN GLY GLN SEQRES 4 A 307 LEU LYS LEU LEU LEU GLY GLU LEU PHE PHE LEU SER LYS SEQRES 5 A 307 LEU GLN ARG HIS GLY ILE LEU ASP GLY ALA THR VAL VAL SEQRES 6 A 307 TYR ILE GLY SER ALA PRO GLY THR HIS ILE ARG TYR LEU SEQRES 7 A 307 ARG ASP HIS PHE TYR ASN LEU GLY VAL ILE ILE LYS TRP SEQRES 8 A 307 MET LEU ILE ASP GLY ARG HIS HIS ASP PRO ILE LEU ASN SEQRES 9 A 307 GLY LEU ARG ASP VAL THR LEU VAL THR ARG PHE VAL ASP SEQRES 10 A 307 GLU GLU TYR LEU ARG SER ILE LYS LYS GLN LEU HIS PRO SEQRES 11 A 307 SER LYS ILE ILE LEU ILE SER ASP VAL ARG SER LYS ARG SEQRES 12 A 307 GLY GLY ASN GLU PRO SER THR ALA ASP LEU LEU SER ASN SEQRES 13 A 307 TYR ALA LEU GLN ASN VAL MET ILE SER ILE LEU ASN PRO SEQRES 14 A 307 VAL ALA SER SER LEU LYS TRP ARG CYS PRO TRP PRO ASP SEQRES 15 A 307 GLN TRP ILE LYS ASP PHE TYR ILE PRO HIS GLY ASN LYS SEQRES 16 A 307 MET LEU GLN PRO PHE ALA PRO SER TYR SER ALA GLU MET SEQRES 17 A 307 ARG LEU LEU SER ILE TYR THR GLY GLU ASN MET ARG LEU SEQRES 18 A 307 THR ARG VAL THR LYS SER ASP ALA VAL ASN TYR GLU LYS SEQRES 19 A 307 LYS MET TYR TYR LEU ASN LYS ILE VAL ARG ASN LYS VAL SEQRES 20 A 307 VAL VAL ASN PHE ASP TYR PRO ASN GLN GLU TYR ASP TYR SEQRES 21 A 307 PHE HIS MET TYR PHE MET LEU ARG THR VAL TYR CYS ASN SEQRES 22 A 307 LYS THR PHE PRO THR THR LYS ALA LYS VAL LEU PHE LEU SEQRES 23 A 307 GLN GLN SER ILE PHE ARG PHE LEU ASN ILE PRO THR THR SEQRES 24 A 307 SER THR GLU LYS VAL SER HIS GLU HET SAH A 400 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *73(H2 O) HELIX 1 1 TYR A 12 ILE A 16 5 5 HELIX 2 2 GLU A 23 GLU A 29 5 7 HELIX 3 3 TYR A 36 HIS A 56 1 21 HELIX 4 4 GLY A 72 GLY A 86 1 15 HELIX 5 5 ASP A 100 ASN A 104 5 5 HELIX 6 6 ASP A 117 HIS A 129 1 13 HELIX 7 7 SER A 149 ASN A 168 1 20 HELIX 8 8 TRP A 180 TRP A 184 5 5 HELIX 9 9 THR A 225 ILE A 242 1 18 HELIX 10 10 VAL A 243 LYS A 246 5 4 HELIX 11 11 GLU A 257 ARG A 268 1 12 HELIX 12 12 THR A 278 ASN A 295 1 18 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 ILE A 89 ASP A 95 1 N LEU A 93 O VAL A 112 SHEET 3 B 7 ALA A 62 ILE A 67 1 N VAL A 64 O LYS A 90 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 LEU A 210 N LEU A 174 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 PRO A 191 0 SHEET 2 C 2 LEU A 221 VAL A 224 -1 O VAL A 224 N PHE A 188 CISPEP 1 ALA A 70 PRO A 71 0 0.02 CISPEP 2 HIS A 129 PRO A 130 0 0.17 SITE 1 AC1 16 GLN A 39 LEU A 42 TYR A 66 GLY A 68 SITE 2 AC1 16 SER A 69 ALA A 70 PRO A 71 GLY A 72 SITE 3 AC1 16 HIS A 74 ASP A 95 ARG A 97 PHE A 115 SITE 4 AC1 16 VAL A 116 ASP A 138 VAL A 139 ARG A 140 CRYST1 84.640 67.940 80.020 90.00 117.92 90.00 C 1 2 1 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 0.011815 0.000000 0.006261 0.00000 SCALE2 0.000000 0.014719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014143 0.00000