HEADER TRANSFERASE 26-JAN-99 1EAM TITLE VACCINIA METHYLTRANSFERASE VP39 MUTANT (EC: 2.7.7.19) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (VP39); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLY(A) POLYMERASE REGULATORY SUBUNIT; COMPND 5 EC: 2.7.7.19; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS; SOURCE 3 ORGANISM_TAXID: 10245; SOURCE 4 STRAIN: BL21 (DE3); SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) KEYWDS METHYLATED GUANOSINE, METHYLTRANSFERASE MUTANT E233A, POLY (A) KEYWDS 2 POLYMERASE, VACCINIA, MRNA PROCESSING, TRANSCRIPTION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.HU,A.E.HODEL,P.D.GERSHON,F.A.QUIOCHO REVDAT 6 27-DEC-23 1EAM 1 REMARK REVDAT 5 03-NOV-21 1EAM 1 REMARK SEQADV REVDAT 4 02-MAR-10 1EAM 1 HETATM REVDAT 3 24-FEB-09 1EAM 1 VERSN REVDAT 2 01-APR-03 1EAM 1 JRNL REVDAT 1 14-JUN-99 1EAM 0 JRNL AUTH G.HU,P.D.GERSHON,A.E.HODEL,F.A.QUIOCHO JRNL TITL MRNA CAP RECOGNITION: DOMINANT ROLE OF ENHANCED STACKING JRNL TITL 2 INTERACTIONS BETWEEN METHYLATED BASES AND PROTEIN AROMATIC JRNL TITL 3 SIDE CHAINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 7149 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10377383 JRNL DOI 10.1073/PNAS.96.13.7149 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)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0001 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.3 REMARK 3 NUMBER OF REFLECTIONS : 22355 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE-R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2354 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 94 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) : 1.556 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-99. REMARK 100 THE DEPOSITION ID IS D_1000000382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 103.0 REMARK 200 PH : 6.5 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18476 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11700 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 42.49900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.75300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.49900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.75300 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 GLU A 25 REMARK 465 SER A 26 REMARK 465 ALA A 27 REMARK 465 ASN A 28 REMARK 465 GLU A 29 REMARK 465 VAL A 30 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 ASP A 17 32.66 -97.33 REMARK 500 ASP A 138 25.77 -141.43 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 DBREF 1EAM A 1 307 UNP P07617 PAP2_VACCV 1 307 SEQADV 1EAM ALA A 233 UNP P07617 GLU 233 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 PHE 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 ALA 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 30 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *94(H2 O) HELIX 1 1 PHE A 13 GLU A 15 5 3 HELIX 2 3 GLN A 37 HIS A 56 1 20 HELIX 3 4 THR A 73 LEU A 85 1 13 HELIX 4 5 PRO A 101 LEU A 103 5 3 HELIX 5 6 GLU A 118 LEU A 128 1 11 HELIX 6 7 THR A 150 LEU A 167 1 18 HELIX 7 8 LYS A 226 LYS A 241 1 16 HELIX 8 9 VAL A 243 ASN A 245 5 3 HELIX 9 10 TYR A 258 THR A 269 1 12 HELIX 10 11 THR A 279 PHE A 293 1 15 SHEET 1 A 7 ASN A 194 MET A 196 0 SHEET 2 A 7 MET A 208 ILE A 213 -1 N LEU A 211 O ASN A 194 SHEET 3 A 7 ALA A 171 TRP A 176 -1 N TRP A 176 O MET A 208 SHEET 4 A 7 ILE A 133 SER A 137 1 N LEU A 135 O ALA A 171 SHEET 5 A 7 ALA A 62 ILE A 67 1 N THR A 63 O ILE A 134 SHEET 6 A 7 ILE A 89 ASP A 95 1 N LYS A 90 O ALA A 62 SHEET 7 A 7 VAL A 109 THR A 113 1 N THR A 110 O TRP A 91 SHEET 1 B 2 PHE A 188 PRO A 191 0 SHEET 2 B 2 LEU A 221 VAL A 224 -1 N VAL A 224 O PHE A 188 CISPEP 1 ALA A 70 PRO A 71 0 0.79 CISPEP 2 HIS A 129 PRO A 130 0 1.05 SITE 1 AC1 19 GLN A 39 LEU A 42 TYR A 66 ILE A 67 SITE 2 AC1 19 GLY A 68 SER A 69 ALA A 70 PRO A 71 SITE 3 AC1 19 GLY A 72 HIS A 74 ILE A 94 ASP A 95 SITE 4 AC1 19 ARG A 97 PHE A 115 VAL A 116 ASP A 138 SITE 5 AC1 19 VAL A 139 ARG A 140 HOH A 471 CRYST1 84.998 67.506 79.919 90.00 117.42 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 0.011765 0.000000 0.006104 0.00000 SCALE2 0.000000 0.014813 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014096 0.00000