HEADER TRANSFERASE 03-JAN-13 2M2U TITLE BINARY COMPLEX OF AFRICAN SWINE FEVER VIRUS POL X WITH MGDGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPAIR DNA POLYMERASE X; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL X; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 3 ORGANISM_TAXID: 10497; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-17B KEYWDS DNA POLYMERASE, NUCLEOTIDYL TRANSFERASE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.WU,M.SU,M.TSAI REVDAT 3 01-MAY-24 2M2U 1 REMARK LINK REVDAT 2 12-NOV-14 2M2U 1 JRNL REVDAT 1 02-APR-14 2M2U 0 JRNL AUTH W.J.WU,M.I.SU,J.L.WU,S.KUMAR,L.H.LIM,C.W.WANG,F.H.NELISSEN, JRNL AUTH 2 M.C.CHEN,J.F.DORELEIJERS,S.S.WIJMENGA,M.D.TSAI JRNL TITL HOW A LOW-FIDELITY DNA POLYMERASE CHOOSES NON-WATSON-CRICK JRNL TITL 2 FROM WATSON-CRICK INCORPORATION. JRNL REF J.AM.CHEM.SOC. V. 136 4927 2014 JRNL REFN ISSN 0002-7863 JRNL PMID 24617852 JRNL DOI 10.1021/JA4102375 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, HADDOCK REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), DR. REMARK 3 ALEXANDRE BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000103138. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN_1, 5 MM [U-100% 13C; U-100% 15N] 2'-DEOXYGUANOSINE-5'- REMARK 210 TRIPHOSPHATE, 10 MM MG2, 10 MM [U-100% 2H] DTT, 50 MM BORATE, 50 REMARK 210 MM POTASSIUM CHLORIDE, 95% H2O/5% D2O; 0.5 MM [U-13C; U-15N; U- REMARK 210 2H] PROTEIN_1, 5 MM 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 10 MM MG2, REMARK 210 10 MM [U-100% 2H] DTT, 50 MM BORATE, 50 MM POTASSIUM CHLORIDE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 850 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 O3G DGT A 201 MG MG A 203 1.28 REMARK 500 OD2 ASP A 51 MG MG A 202 1.52 REMARK 500 OD2 ASP A 100 MG MG A 202 1.56 REMARK 500 OD1 ASP A 49 MG MG A 202 1.60 REMARK 500 O ASP A 49 MG MG A 203 1.63 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 1 ASN A 48 -76.85 -78.89 REMARK 500 1 GLN A 146 -7.47 75.34 REMARK 500 1 THR A 154 -16.27 -144.35 REMARK 500 1 ARG A 173 145.37 67.33 REMARK 500 2 ASN A 48 -54.09 -122.53 REMARK 500 2 ASN A 134 36.03 74.56 REMARK 500 2 ASN A 145 -64.40 71.70 REMARK 500 2 GLN A 146 8.72 -167.87 REMARK 500 2 ARG A 173 130.10 61.63 REMARK 500 3 GLU A 43 51.55 72.69 REMARK 500 3 THR A 117 -73.51 -50.74 REMARK 500 3 ASN A 134 35.39 74.30 REMARK 500 3 THR A 154 -5.29 -142.81 REMARK 500 3 ARG A 173 126.08 66.79 REMARK 500 4 THR A 117 -72.06 -48.78 REMARK 500 4 ASN A 134 38.72 73.54 REMARK 500 4 GLN A 146 -6.81 68.92 REMARK 500 4 THR A 154 -14.41 -142.03 REMARK 500 4 ARG A 173 139.98 68.40 REMARK 500 5 PRO A 57 0.53 -69.85 REMARK 500 5 THR A 117 -73.05 -52.07 REMARK 500 5 ASN A 134 31.99 74.26 REMARK 500 5 ASN A 145 -70.09 67.58 REMARK 500 5 GLN A 146 0.13 -152.91 REMARK 500 5 THR A 154 -8.40 -147.65 REMARK 500 5 ARG A 173 147.76 61.00 REMARK 500 6 GLU A 43 50.74 72.80 REMARK 500 6 LYS A 72 108.15 -56.59 REMARK 500 6 ASN A 134 41.91 72.59 REMARK 500 6 ASN A 145 -71.77 65.54 REMARK 500 6 ARG A 173 161.83 55.23 REMARK 500 7 THR A 117 -71.21 -52.47 REMARK 500 7 GLN A 146 -1.81 75.50 REMARK 500 7 THR A 154 -11.21 -148.12 REMARK 500 7 ARG A 173 145.38 65.16 REMARK 500 8 THR A 117 -73.83 -49.17 REMARK 500 8 ASN A 134 35.71 73.01 REMARK 500 8 GLN A 146 -6.05 77.73 REMARK 500 8 THR A 154 -11.57 -140.21 REMARK 500 8 ARG A 173 134.30 61.52 REMARK 500 9 ASN A 134 42.61 72.81 REMARK 500 9 GLN A 146 -2.22 72.49 REMARK 500 9 ARG A 173 -133.20 -87.77 REMARK 500 10 GLU A 43 54.65 73.06 REMARK 500 10 ASN A 134 42.43 73.35 REMARK 500 10 GLN A 146 -5.23 68.21 REMARK 500 10 PRO A 150 -177.71 -69.90 REMARK 500 10 ARG A 173 138.90 59.50 REMARK 500 11 ASN A 48 -61.45 -91.60 REMARK 500 11 THR A 117 -72.94 -51.79 REMARK 500 REMARK 500 THIS ENTRY HAS 98 RAMACHANDRAN OUTLIERS. 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 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD2 REMARK 620 2 ASP A 49 OD1 40.6 REMARK 620 3 ASP A 51 OD1 101.0 62.7 REMARK 620 4 DGT A 201 O2B 155.0 142.0 81.0 REMARK 620 5 DGT A 201 O3A 99.0 89.9 59.1 60.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 51 OD1 REMARK 620 2 DGT A 201 O1A 71.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18934 RELATED DB: BMRB REMARK 900 RELATED ID: 2M2T RELATED DB: PDB REMARK 900 RELATED ID: 2M2V RELATED DB: PDB REMARK 900 RELATED ID: 2M2W RELATED DB: PDB DBREF 2M2U A 1 174 UNP P42494 DPOLX_ASFB7 1 174 SEQRES 1 A 174 MET LEU THR LEU ILE GLN GLY LYS LYS ILE VAL ASN HIS SEQRES 2 A 174 LEU ARG SER ARG LEU ALA PHE GLU TYR ASN GLY GLN LEU SEQRES 3 A 174 ILE LYS ILE LEU SER LYS ASN ILE VAL ALA VAL GLY SER SEQRES 4 A 174 LEU ARG ARG GLU GLU LYS MET LEU ASN ASP VAL ASP LEU SEQRES 5 A 174 LEU ILE ILE VAL PRO GLU LYS LYS LEU LEU LYS HIS VAL SEQRES 6 A 174 LEU PRO ASN ILE ARG ILE LYS GLY LEU SER PHE SER VAL SEQRES 7 A 174 LYS VAL CYS GLY GLU ARG LYS CYS VAL LEU PHE ILE GLU SEQRES 8 A 174 TRP GLU LYS LYS THR TYR GLN LEU ASP LEU PHE THR ALA SEQRES 9 A 174 LEU ALA GLU GLU LYS PRO TYR ALA ILE PHE HIS PHE THR SEQRES 10 A 174 GLY PRO VAL SER TYR LEU ILE ARG ILE ARG ALA ALA LEU SEQRES 11 A 174 LYS LYS LYS ASN TYR LYS LEU ASN GLN TYR GLY LEU PHE SEQRES 12 A 174 LYS ASN GLN THR LEU VAL PRO LEU LYS ILE THR THR GLU SEQRES 13 A 174 LYS GLU LEU ILE LYS GLU LEU GLY PHE THR TYR ARG ILE SEQRES 14 A 174 PRO LYS LYS ARG LEU HET DGT A 201 43 HET MG A 202 1 HET MG A 203 1 HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 DGT C10 H16 N5 O13 P3 FORMUL 3 MG 2(MG 2+) HELIX 1 1 LEU A 4 ARG A 17 1 14 HELIX 2 2 GLY A 38 GLU A 43 1 6 HELIX 3 3 GLU A 58 HIS A 64 1 7 HELIX 4 4 GLU A 108 GLY A 118 1 11 HELIX 5 5 PRO A 119 LYS A 133 1 15 HELIX 6 6 THR A 155 GLY A 164 1 10 HELIX 7 7 ILE A 169 ARG A 173 5 5 SHEET 1 A 2 LEU A 2 THR A 3 0 SHEET 2 A 2 MET A 46 LEU A 47 -1 O LEU A 47 N LEU A 2 SHEET 1 B 3 GLN A 25 ILE A 29 0 SHEET 2 B 3 LEU A 18 TYR A 22 -1 N PHE A 20 O ILE A 27 SHEET 3 B 3 ASN A 68 ILE A 71 -1 O ARG A 70 N ALA A 19 SHEET 1 C 5 ILE A 34 VAL A 37 0 SHEET 2 C 5 VAL A 50 VAL A 56 -1 O ASP A 51 N VAL A 37 SHEET 3 C 5 LYS A 95 LEU A 105 1 O ASP A 100 N LEU A 52 SHEET 4 C 5 LYS A 85 TRP A 92 -1 N ILE A 90 O TYR A 97 SHEET 5 C 5 SER A 75 CYS A 81 -1 N LYS A 79 O VAL A 87 SHEET 1 D 3 TYR A 135 ASN A 138 0 SHEET 2 D 3 GLY A 141 LYS A 144 -1 O PHE A 143 N LYS A 136 SHEET 3 D 3 THR A 147 VAL A 149 -1 O VAL A 149 N LEU A 142 LINK OD2 ASP A 49 MG MG A 203 1555 1555 3.29 LINK OD1 ASP A 49 MG MG A 203 1555 1555 2.76 LINK OD1 ASP A 51 MG MG A 202 1555 1555 2.89 LINK OD1 ASP A 51 MG MG A 203 1555 1555 2.51 LINK O1A DGT A 201 MG MG A 202 1555 1555 2.81 LINK O2B DGT A 201 MG MG A 203 1555 1555 2.15 LINK O3A DGT A 201 MG MG A 203 1555 1555 2.75 SITE 1 AC1 15 VAL A 37 GLY A 38 SER A 39 ARG A 42 SITE 2 AC1 15 LEU A 47 ASN A 48 ASP A 49 ASP A 51 SITE 3 AC1 15 LYS A 85 HIS A 115 PHE A 116 GLY A 118 SITE 4 AC1 15 VAL A 120 MG A 202 MG A 203 SITE 1 AC2 5 ASP A 49 ASP A 51 ASP A 100 DGT A 201 SITE 2 AC2 5 MG A 203 SITE 1 AC3 4 ASP A 49 ASP A 51 DGT A 201 MG A 202 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1