4AMQ - Header Asymmetric Unit

HEADER TRANSFERASE 13-MAR-12 4AMQ

TITLE A MEGAVIRIDAE ORFAN GENE ENCODES A NEW NUCLEOTIDYL TRANSFERASE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: L544; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACANTHAMOEBA POLYPHAGA MIMIVIRUS; SOURCE 3 ORGANISM_COMMON: MIMIVIRUS; SOURCE 4 ORGANISM_TAXID: 212035; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST17

KEYWDS TRANSFERASE, MIMIVIRUS, MG662, TRANSCRIPTION COUPLED DNA REPAIR

EXPDTA X-RAY DIFFRACTION

AUTHOR A.LARTIGUE,J.M.CLAVERIE,S.PRIET,C.ABERGEL

REVDAT 1 20-MAR-13 4AMQ 0

JRNL AUTH A.CIACCAFAVA,A.LARTIGUE,P.MANSUELLE,S.JEUDY,C.ABERGEL JRNL TITL A MEGAVIRIDAE ORPHAN GENE ENCODES A NEW NUCLEOTIDYL JRNL TITL 2 TRANSFERASE JRNL REF TO BE PUBLISHED JRNL REFN

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.CIACCAFAVA,A.LARTIGUE,P.MANSUELLE,S.JEUDY,C.ABERGEL REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF A POSSIBLE REMARK 1 TITL 2 TRANSCRIPTION FACTOR ENCODED BY THE MIMIVIRUS L544 GENE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 67 922 2011 REMARK 1 REFN ISSN 1744-3091 REMARK 1 PMID 21821896 REMARK 1 DOI 10.1107/S1744309111020847

REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.170 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.290 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.03 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.15 REMARK 3 NUMBER OF REFLECTIONS : 20963 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2206 REMARK 3 R VALUE (WORKING SET) : 0.2192 REMARK 3 FREE R VALUE : 0.2442 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.2 REMARK 3 FREE R VALUE TEST SET COUNT : 1088 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.2929 - 4.3361 0.90 2539 137 0.2023 0.2030 REMARK 3 2 4.3361 - 3.4434 0.93 2535 131 0.1935 0.2107 REMARK 3 3 3.4434 - 3.0086 0.94 2538 148 0.2239 0.2681 REMARK 3 4 3.0086 - 2.7338 0.94 2494 141 0.2444 0.2659 REMARK 3 5 2.7338 - 2.5379 0.94 2529 139 0.2324 0.3292 REMARK 3 6 2.5379 - 2.3884 0.93 2475 134 0.2354 0.2847 REMARK 3 7 2.3884 - 2.2688 0.90 2394 124 0.2463 0.2716 REMARK 3 8 2.2688 - 2.1701 0.89 2371 134 0.2457 0.2966 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.363 REMARK 3 B_SOL : 50.034 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.31 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.3615 REMARK 3 B22 (A**2) : 1.4128 REMARK 3 B33 (A**2) : -9.7743 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 2926 REMARK 3 ANGLE : 0.678 3949 REMARK 3 CHIRALITY : 0.048 448 REMARK 3 PLANARITY : 0.004 489 REMARK 3 DIHEDRAL : 12.563 1122 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: - LOOP RESIDUES 120 TO 126 ARE REMARK 3 DISORDERED - LINKER RESIDUES 198 TO 210 ARE DISORDERED - REMARK 3 RESIDUES 360 TO THE END ARE DISORDERED

REMARK 4 REMARK 4 4AMQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-12. REMARK 100 THE PDBE ID CODE IS EBI-51654.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.17 REMARK 200 RESOLUTION RANGE LOW (A) : 50.40 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NONE REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.8 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.80 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.7 REMARK 200 R MERGE FOR SHELL (I) : 0.36 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION: 10 MG/ML REMARK 280 IN 10 MM CHES BUFFER PH 9.0 RESERVOIR: 4 TO 12% PEG 4000, REMARK 280 0.1 M SODIUM CACODYLATE BETWEEN PH 6 AND 7, 0.1 M MNCL2

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 76.49700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.49700 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.22250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.54600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.22250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.54600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.49700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.22250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.54600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.49700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.22250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.54600 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 HOH A2016 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2090 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2098 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 SER A -21 REMARK 465 TYR A -20 REMARK 465 TYR A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 LEU A -12 REMARK 465 GLU A -11 REMARK 465 SER A -10 REMARK 465 THR A -9 REMARK 465 SER A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 LYS A -5 REMARK 465 LYS A -4 REMARK 465 ALA A -3 REMARK 465 GLY A -2 REMARK 465 LEU A -1 REMARK 465 LEU A 119 REMARK 465 SER A 120 REMARK 465 LYS A 121 REMARK 465 TYR A 122 REMARK 465 GLN A 123 REMARK 465 ASP A 124 REMARK 465 ASP A 125 REMARK 465 LEU A 126 REMARK 465 ILE A 199 REMARK 465 ASN A 200 REMARK 465 LEU A 201 REMARK 465 ILE A 202 REMARK 465 THR A 203 REMARK 465 ALA A 204 REMARK 465 TYR A 205 REMARK 465 GLN A 206 REMARK 465 ASN A 207 REMARK 465 ALA A 208 REMARK 465 ALA A 209 REMARK 465 GLU A 360 REMARK 465 GLU A 361 REMARK 465 GLU A 362 REMARK 465 HIS A 363 REMARK 465 VAL A 364 REMARK 465 LEU A 365 REMARK 465 GLN A 366 REMARK 465 SER A 367 REMARK 465 GLY A 368 REMARK 465 GLY A 369 REMARK 465 ILE A 370 REMARK 465 ASN A 371 REMARK 465 PHE A 372 REMARK 465 GLU A 373 REMARK 465 SER A 374 REMARK 465 THR A 375 REMARK 465 ASN A 376 REMARK 465 PHE A 377 REMARK 465 LEU A 378 REMARK 465 THR A 379 REMARK 465 LYS A 380 REMARK 465 LYS A 381 REMARK 465 LYS A 382 REMARK 465 LEU A 383 REMARK 465 ILE A 384 REMARK 465 TYR A 385

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 OD2 ASP A 288 O HOH A 2085 2.10 REMARK 500 O HOH A 2016 O HOH A 2046 2.12 REMARK 500 O HOH A 2060 O HOH A 2061 2.17 REMARK 500 O HOH A 2108 O HOH A 2109 1.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2016 O HOH A 2046 3655 2.12 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 ILE A 16 -61.48 -95.12 REMARK 500 ASN A 117 69.08 -169.69 REMARK 500 GLU A 184 -93.90 -126.59 REMARK 500 SER A 219 -82.91 -77.08 REMARK 500 LYS A 220 35.15 -151.33 REMARK 500 SER A 307 -6.54 -58.31 REMARK 500 REMARK 500 REMARK: NULL

REMARK 600 REMARK 600 HETEROGEN REMARK 600 MANGANESE (II) ION (MN): LOCATED IN THE NUCLEOTIDYL REMARK 600 TRANSFERASE CATALYTIC DOMAIN

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 MN A 639 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2030 O REMARK 620 2 ASP A 44 OD1 77.0 REMARK 620 3 ASP A 46 OD2 134.9 142.1 REMARK 620 4 ASP A 44 OD2 115.5 51.8 91.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 640 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 46 OD1 REMARK 620 2 ASP A 191 OD2 100.0 REMARK 620 3 ASP A 44 OD2 79.7 125.0 REMARK 620 4 HOH A2031 O 175.6 84.2 99.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1360 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 77 O REMARK 620 2 ASP A 74 O 76.4 REMARK 620 3 HOH A2042 O 110.0 169.4 REMARK 620 4 HOH A2045 O 94.6 74.8 112.3 REMARK 620 5 PHE A 71 O 108.1 84.2 85.7 144.4 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 MN A 639 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 640 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1360

REMARK 999 REMARK 999 SEQUENCE REMARK 999 ADDITIONAL N-TERMINAL HIS-TAG, LEU -1 REPLACES INITIATION REMARK 999 METHIONINE. NUCLEOTIDYL TRANSFERASE CATALYTIC DOMAIN IS REMARK 999 RESIDUES 1-197.

DBREF 4AMQ A -1 385 UNP Q5UQA5 YL544_MIMIV 1 387

SEQADV 4AMQ SER A -21 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ TYR A -20 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ TYR A -19 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ HIS A -18 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ HIS A -17 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ HIS A -16 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ HIS A -15 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ HIS A -14 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ HIS A -13 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ LEU A -12 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ GLU A -11 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ SER A -10 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ THR A -9 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ SER A -8 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ LEU A -7 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ TYR A -6 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ LYS A -5 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ LYS A -4 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ ALA A -3 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ GLY A -2 UNP Q5UQA5 EXPRESSION TAG SEQADV 4AMQ LEU A -1 UNP Q5UQA5 MET 1 SEE REMARK 999

SEQRES 1 A 407 SER TYR TYR HIS HIS HIS HIS HIS HIS LEU GLU SER THR SEQRES 2 A 407 SER LEU TYR LYS LYS ALA GLY LEU ARG MET LEU ILE PHE SEQRES 3 A 407 THR TYR LYS LEU GLU ARG TYR ILE LYS ASN LYS ILE LEU SEQRES 4 A 407 PRO LYS ILE LEU VAL VAL PRO ASP ARG ASP LYS TYR GLN SEQRES 5 A 407 ILE LYS GLY SER PHE ARG ARG ARG ILE PRO TYR ILE THR SEQRES 6 A 407 ASP ILE ASP ILE VAL ASN ASN VAL HIS PRO GLU TYR ASP SEQRES 7 A 407 ASP THR ASN ILE TYR GLN ARG ILE VAL ASP LEU ILE ASN SEQRES 8 A 407 SER PHE THR ASN ASP ASN GLN ILE LYS LEU ILE TYR VAL SEQRES 9 A 407 ILE CYS GLY THR ASP ASP ARG PHE LEU LEU THR GLU TYR SEQRES 10 A 407 SER ASP GLU GLU ILE GLU LYS ILE LYS ILE LEU LEU ASN SEQRES 11 A 407 PRO THR GLU LEU VAL GLU LEU ASN ASN VAL LEU SER LYS SEQRES 12 A 407 TYR GLN ASP ASP LEU ASN LYS LYS VAL PHE TYR ILE ASN SEQRES 13 A 407 GLU ILE ILE TRP ASP LEU TYR LYS LEU ARG TRP THR SER SEQRES 14 A 407 SER GLU VAL LEU ALA GLY LYS LYS ILE LEU ARG GLY GLY SEQRES 15 A 407 ILE GLU VAL SER PHE GLN ASP VAL VAL LYS ASN ASN SER SEQRES 16 A 407 ILE LEU LEU LEU GLN TYR PHE VAL LYS ILE GLU TYR TYR SEQRES 17 A 407 PRO ILE GLY PHE ASP ILE ALA VAL ARG TYR LYS PRO ILE SEQRES 18 A 407 ASN LEU ILE THR ALA TYR GLN ASN ALA ALA PHE TYR GLN SEQRES 19 A 407 LEU LYS LEU ALA ASN TYR SER LYS GLU TYR TYR PHE MET SEQRES 20 A 407 LEU PHE PRO LEU ARG PHE TYR PHE LYS ASN ASP PRO THR SEQRES 21 A 407 ILE SER LYS GLN LEU GLU TYR ILE ILE GLU THR LYS PHE SEQRES 22 A 407 GLY LEU TYR LYS GLN LEU LEU VAL ARG ILE ASP SER TYR SEQRES 23 A 407 ARG THR ILE TYR GLU SER GLY ASN LEU ASP LEU ASP THR SEQRES 24 A 407 ALA LYS SER ILE ILE ILE SER ILE ILE LYS ASP ILE ARG SEQRES 25 A 407 LYS LEU ASN GLY ILE ASP MET ASN ILE ILE ASP LYS ILE SEQRES 26 A 407 GLN GLU VAL SER ASN ASN SER ALA GLY GLN ASP LYS ILE SEQRES 27 A 407 ILE ALA TRP ASN THR LEU LEU THR GLN LEU TYR THR ASN SEQRES 28 A 407 ILE ASN LYS SER VAL ASN LYS GLN SER LYS LYS TYR PHE SEQRES 29 A 407 THR ARG TYR ILE ASN ILE ILE PRO LYS GLU ASP ARG LYS SEQRES 30 A 407 LEU CYS CYS LEU GLU GLU GLU HIS VAL LEU GLN SER GLY SEQRES 31 A 407 GLY ILE ASN PHE GLU SER THR ASN PHE LEU THR LYS LYS SEQRES 32 A 407 LYS LEU ILE TYR

HET MN A 639 1 HET MN A 640 1 HET MG A1360 1

HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION

FORMUL 2 MN 2(MN 2+) FORMUL 3 MG MG 2+ FORMUL 4 HOH *122(H2 O)

HELIX 1 1 THR A 5 ILE A 16 1 12 HELIX 2 2 ILE A 16 LEU A 21 1 6 HELIX 3 3 ASP A 25 ASP A 27 5 3 HELIX 4 4 GLY A 33 ARG A 37 1 5 HELIX 5 5 ASN A 59 THR A 72 1 14 HELIX 6 6 ASP A 88 LEU A 91 5 4 HELIX 7 7 TYR A 95 LYS A 104 1 10 HELIX 8 8 PRO A 109 GLU A 114 1 6 HELIX 9 9 LYS A 129 TYR A 141 1 13 HELIX 10 10 THR A 146 GLY A 153 1 8 HELIX 11 11 ARG A 158 GLY A 160 5 3 HELIX 12 12 PHE A 165 ASN A 171 1 7 HELIX 13 13 LYS A 214 TYR A 218 5 5 HELIX 14 14 MET A 225 PHE A 233 1 9 HELIX 15 15 ASP A 236 THR A 249 1 14 HELIX 16 16 PHE A 251 GLY A 271 1 21 HELIX 17 17 ASP A 274 ARG A 290 1 17 HELIX 18 18 ASP A 296 SER A 310 1 15 HELIX 19 19 ALA A 311 ASN A 347 1 37 HELIX 20 20 PRO A 350 LYS A 355 1 6

SHEET 1 AA 6 TYR A 29 LYS A 32 0 SHEET 2 AA 6 ASP A 44 ASN A 50 -1 O ASP A 46 N LYS A 32 SHEET 3 AA 6 PRO A 187 ARG A 195 1 O GLY A 189 N ILE A 45 SHEET 4 AA 6 ILE A 174 LYS A 182 -1 O LEU A 175 N VAL A 194 SHEET 5 AA 6 ILE A 77 THR A 86 -1 O LYS A 78 N PHE A 180 SHEET 6 AA 6 LYS A 142 TRP A 145 -1 O LEU A 143 N CYS A 84 SHEET 1 AB 2 LYS A 154 ILE A 156 0 SHEET 2 AB 2 GLU A 162 SER A 164 -1 O VAL A 163 N LYS A 155

SSBOND 1 CYS A 357 CYS A 358 1555 1555 2.01

LINK MN MN A 639 O HOH A2030 1555 1555 2.26 LINK MN MN A 639 OD1 ASP A 44 1555 1555 2.38 LINK MN MN A 639 OD2 ASP A 46 1555 1555 2.61 LINK MN MN A 639 OD2 ASP A 44 1555 1555 2.61 LINK MN MN A 640 OD1 ASP A 46 1555 1555 2.30 LINK MN MN A 640 OD2 ASP A 191 1555 1555 2.56 LINK MN MN A 640 OD2 ASP A 44 1555 1555 2.20 LINK MN MN A 640 O HOH A2031 1555 1555 2.56 LINK MG MG A1360 O ASP A 74 1555 1555 2.59 LINK MG MG A1360 O HOH A2042 1555 1555 2.56 LINK MG MG A1360 O HOH A2045 1555 1555 2.45 LINK MG MG A1360 O PHE A 71 1555 1555 2.62 LINK MG MG A1360 O ILE A 77 1555 1555 2.45

CISPEP 1 HIS A 52 PRO A 53 0 4.06 CISPEP 2 ASN A 117 VAL A 118 0 6.35 CISPEP 3 CYS A 357 CYS A 358 0 -0.06

SITE 1 AC1 4 ASP A 44 ASP A 46 MN A 640 HOH A2030 SITE 1 AC2 6 ASP A 44 ASP A 46 ASP A 191 MN A 639 SITE 2 AC2 6 HOH A2031 HOH A2032 SITE 1 AC3 5 PHE A 71 ASP A 74 ILE A 77 HOH A2042 SITE 2 AC3 5 HOH A2045

CRYST1 60.445 91.092 152.994 90.00 90.00 90.00 C 2 2 21 8

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 0.016544 0.000000 0.000000 0.00000

SCALE2 0.000000 0.010978 0.000000 0.00000

SCALE3 0.000000 0.000000 0.006536 0.00000