HEADER TRANSFERASE 16-NOV-10 2XY8 TITLE PARAMAGNETIC-BASED NMR STRUCTURE OF THE COMPLEX BETWEEN THE N- TITLE 2 TERMINAL EPSILON DOMAIN AND THE THETA DOMAIN OF THE DNA POLYMERASE TITLE 3 III COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE III SUBUNIT EPSILON; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXONUCLEASE DOMAIN, RESIDUES 1-186; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA POLYMERASE III SUBUNIT THETA; COMPND 9 CHAIN: B; COMPND 10 EC: 2.7.7.7; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TRANSFERASE, DOCKING, EXPERIMENTAL RESTRAINTS, HADDOCK PROGRAM EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR C.SCHMITZ,A.M.J.J.BONVIN REVDAT 4 15-MAY-24 2XY8 1 REMARK LINK REVDAT 3 17-JAN-18 2XY8 1 JRNL REVDAT 2 03-AUG-11 2XY8 1 JRNL REMARK VERSN REVDAT 1 29-JUN-11 2XY8 0 JRNL AUTH C.SCHMITZ,A.M.J.J.BONVIN JRNL TITL PROTEIN-PROTEIN HADDOCKING USING EXCLUSIVELY PSEUDOCONTACT JRNL TITL 2 SHIFTS. JRNL REF J.BIOMOL.NMR V. 50 263 2011 JRNL REFN ISSN 0925-2738 JRNL PMID 21626213 JRNL DOI 10.1007/S10858-011-9514-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.SCHMITZ,M.J.STANTON-COOK,X.C.SU,G.OTTING,T.HUBER REMARK 1 TITL NUMBAT: AN INTERACTIVE SOFTWARE TOOL FOR FITTING REMARK 1 TITL 2 DELTACHI-TENSORS TO MOLECULAR COORDINATES USING REMARK 1 TITL 3 PSEUDOCONTACT SHIFTS REMARK 1 REF J.BIOMOL.NMR V. 41 179 2008 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 18574699 REMARK 1 DOI 10.1007/S10858-008-9249-Z REMARK 1 REFERENCE 2 REMARK 1 AUTH G.PINTACUDA,A.Y.PARK,M.A.KENIRY,N.E.DIXON,G.OTTING REMARK 1 TITL LANTHANIDE LABELING OFFERS FAST NMR APPROACH TO 3D STRUCTURE REMARK 1 TITL 2 DETERMINATIONS OF PROTEIN-PROTEIN COMPLEXES REMARK 1 REF J.AM.CHEM.SOC. V. 128 3696 2006 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 16536542 REMARK 1 DOI 10.1021/JA057008Z REMARK 1 REFERENCE 3 REMARK 1 AUTH S.J.DE VRIES,A.D.J.VAN DIJK,M.KRZEMINSKI,M.VAN DIJK, REMARK 1 AUTH 2 A.THUREAU,V.HSU,T.WASSENAAR,A.M.J.J.BONVIN REMARK 1 TITL HADDOCK VERSUS HADDOCK: NEW FEATURES AND PERFORMANCE OF REMARK 1 TITL 2 HADDOCK2.0 ON THE CAPRI TARGETS. REMARK 1 REF PROTEINS V. 69 726 2007 REMARK 1 REFN ISSN 0887-3585 REMARK 1 PMID 17803234 REMARK 1 DOI 10.1002/PROT.21723 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : A.T.BRUNGER,P.D.ADAMS,G.M.CLORE, REMARK 3 W.L.DELANO,P.GROS,R.W.GROSSE-KUNSTLEVE, J.-S.JIANG, REMARK 3 J.KUSZEWSKI,M.NILGES,N.S.PANNU, R.J.READ,L.M.RICE, REMARK 3 T.SIMONSON,G.L.WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RUNNING WITHIN HADDOCK2.1-PARA BETA. REMARK 3 REFINEMENT DETAILS CAN BE FOUND AT THE FOLLOWING PUBLICATION: DE REMARK 3 VRIES ET AL. PROTEINS 2007 (REFERENCE 3 IN REMARK 1). REMARK 4 REMARK 4 2XY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290046221. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK2.1-PARA BETA BETA REMARK 210 METHOD USED : DATA-DRIVEN FLEXIBLE DOCKING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TOP 10 STRUCTURES OF THE BEST REMARK 210 CLUSTER REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE COMPLEX WAS DOCKED USING PSEUDOCONTACT SHIFT ( PCS) REMARK 210 RESTRAINTS.THE CONTENTS OF THE SAMPLE ARE SIMILAR TO THAT REMARK 210 DESCRIBED IN LANTHANIDE LABELING OFFERS-FAST NMR APPROACH TO 3D REMARK 210 STRUCTRE DETERMINATIONS OF PROTEIN-PROTEIN COMPLEXES. PINTACUDA REMARK 210 ET ALL. JACS 2006 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 ALA A 4 REMARK 465 ILE A 5 REMARK 465 THR A 6 REMARK 465 GLN A 182 REMARK 465 THR A 183 REMARK 465 SER A 184 REMARK 465 MET A 185 REMARK 465 ALA A 186 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 LYS B 3 REMARK 465 ASN B 4 REMARK 465 LEU B 5 REMARK 465 ALA B 6 REMARK 465 LYS B 7 REMARK 465 LEU B 8 REMARK 465 ASP B 9 REMARK 465 TYR B 71 REMARK 465 GLU B 72 REMARK 465 PRO B 73 REMARK 465 LYS B 74 REMARK 465 LEU B 75 REMARK 465 LYS B 76 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLY A 181 CA C O 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 HZ1 LYS A 29 OE1 GLU A 110 1.57 REMARK 500 OE2 GLU A 32 HE2 HIS A 49 1.57 REMARK 500 HG1 THR A 78 OE1 GLU A 81 1.58 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 HIS A 66 14.01 -144.40 REMARK 500 1 ASN A 99 55.54 72.64 REMARK 500 1 LYS A 158 43.67 -98.50 REMARK 500 1 ARG B 30 56.16 -141.53 REMARK 500 1 LEU B 66 -91.41 64.47 REMARK 500 1 SER B 67 -75.89 -123.94 REMARK 500 1 ARG B 68 94.66 62.36 REMARK 500 2 PRO A 77 -170.00 -73.26 REMARK 500 2 ASN A 143 30.06 -99.79 REMARK 500 2 LYS A 158 58.85 -96.96 REMARK 500 2 PRO B 45 -179.37 -67.67 REMARK 500 2 LEU B 66 -74.37 67.97 REMARK 500 2 SER B 67 -81.18 -122.96 REMARK 500 3 THR A 15 -168.98 -117.91 REMARK 500 3 GLU A 26 107.07 -57.08 REMARK 500 3 ARG A 56 -166.34 -167.48 REMARK 500 3 ASN A 99 76.19 87.50 REMARK 500 3 TYR B 31 40.04 -72.90 REMARK 500 3 LEU B 66 -71.39 68.90 REMARK 500 3 SER B 67 -87.98 -130.35 REMARK 500 4 ASP A 55 -41.06 71.66 REMARK 500 4 ASN A 99 60.62 72.09 REMARK 500 4 LYS A 158 33.96 -90.22 REMARK 500 4 TYR B 31 24.77 -74.27 REMARK 500 4 ARG B 68 -167.95 -119.99 REMARK 500 5 THR A 15 -168.06 -110.73 REMARK 500 5 ASN A 99 71.39 76.28 REMARK 500 5 LYS A 158 41.21 -93.12 REMARK 500 5 PRO B 34 73.26 -69.93 REMARK 500 5 LEU B 48 36.56 -144.30 REMARK 500 5 ASN B 65 41.67 -140.47 REMARK 500 6 GLU A 26 102.96 -54.82 REMARK 500 6 ASN A 99 47.18 75.07 REMARK 500 6 TYR B 31 40.17 -82.19 REMARK 500 6 PRO B 45 -179.85 -69.00 REMARK 500 6 LEU B 66 -52.14 70.27 REMARK 500 6 SER B 67 -54.32 -152.20 REMARK 500 7 THR A 15 -166.69 -117.79 REMARK 500 7 ASN A 99 45.71 72.70 REMARK 500 7 ASN A 143 33.17 -91.14 REMARK 500 7 ARG B 30 42.10 -106.37 REMARK 500 7 PRO B 34 106.44 -59.98 REMARK 500 7 VAL B 35 111.45 -162.58 REMARK 500 7 PRO B 45 107.17 -58.42 REMARK 500 7 LEU B 66 -79.97 -71.51 REMARK 500 7 SER B 67 -76.08 68.44 REMARK 500 7 ARG B 68 90.24 62.74 REMARK 500 8 ASP A 55 -44.77 73.85 REMARK 500 8 ASP A 75 35.77 -96.25 REMARK 500 8 ASN A 99 51.79 74.98 REMARK 500 REMARK 500 THIS ENTRY HAS 65 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 CA A 190 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD2 REMARK 620 2 ASP A 12 OD1 47.8 REMARK 620 3 GLU A 14 OE2 104.3 137.2 REMARK 620 4 ASP A 167 OD2 107.8 107.4 112.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 190 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MGZ RELATED DB: PDB REMARK 900 MODEL FOR THE CATALYTIC DOMAIN OF THE PROOFREADING EPSILONSUBUNIT REMARK 900 OF E. COLI DNA POLYMERASE III BASED ON NMRSTRUCTURAL DATA REMARK 900 RELATED ID: 1J53 RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-TERMINAL EXONUCLEASE DOMAIN OF THEEPSILON REMARK 900 SUBUNIT OF E.COLI DNA POLYMERASE III AT PH 8.5 REMARK 900 RELATED ID: 1J54 RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-TERMINAL EXONUCLEASE DOMAIN OF THEEPSILON REMARK 900 SUBUNIT OF E.COLI DNA POLYMERASE III AT PH 5.8 DBREF 2XY8 A 1 186 UNP P03007 DPO3E_ECOLI 1 186 DBREF 2XY8 B 1 76 UNP P0ABT0 HOLE_ECO57 1 76 SEQRES 1 A 186 MET SER THR ALA ILE THR ARG GLN ILE VAL LEU ASP THR SEQRES 2 A 186 GLU THR THR GLY MET ASN GLN ILE GLY ALA HIS TYR GLU SEQRES 3 A 186 GLY HIS LYS ILE ILE GLU ILE GLY ALA VAL GLU VAL VAL SEQRES 4 A 186 ASN ARG ARG LEU THR GLY ASN ASN PHE HIS VAL TYR LEU SEQRES 5 A 186 LYS PRO ASP ARG LEU VAL ASP PRO GLU ALA PHE GLY VAL SEQRES 6 A 186 HIS GLY ILE ALA ASP GLU PHE LEU LEU ASP LYS PRO THR SEQRES 7 A 186 PHE ALA GLU VAL ALA ASP GLU PHE MET ASP TYR ILE ARG SEQRES 8 A 186 GLY ALA GLU LEU VAL ILE HIS ASN ALA ALA PHE ASP ILE SEQRES 9 A 186 GLY PHE MET ASP TYR GLU PHE SER LEU LEU LYS ARG ASP SEQRES 10 A 186 ILE PRO LYS THR ASN THR PHE CYS LYS VAL THR ASP SER SEQRES 11 A 186 LEU ALA VAL ALA ARG LYS MET PHE PRO GLY LYS ARG ASN SEQRES 12 A 186 SER LEU ASP ALA LEU CYS ALA ARG TYR GLU ILE ASP ASN SEQRES 13 A 186 SER LYS ARG THR LEU HIS GLY ALA LEU LEU ASP ALA GLN SEQRES 14 A 186 ILE LEU ALA GLU VAL TYR LEU ALA MET THR GLY GLY GLN SEQRES 15 A 186 THR SER MET ALA SEQRES 1 B 76 MET LEU LYS ASN LEU ALA LYS LEU ASP GLN THR GLU MET SEQRES 2 B 76 ASP LYS VAL ASN VAL ASP LEU ALA ALA ALA GLY VAL ALA SEQRES 3 B 76 PHE LYS GLU ARG TYR ASN MET PRO VAL ILE ALA GLU ALA SEQRES 4 B 76 VAL GLU ARG GLU GLN PRO GLU HIS LEU ARG SER TRP PHE SEQRES 5 B 76 ARG GLU ARG LEU ILE ALA HIS ARG LEU ALA SER VAL ASN SEQRES 6 B 76 LEU SER ARG LEU PRO TYR GLU PRO LYS LEU LYS HET CA A 190 1 HETNAM CA CALCIUM ION FORMUL 3 CA CA 2+ HELIX 1 1 ASP A 59 GLY A 67 1 9 HELIX 2 2 ALA A 69 LEU A 73 5 5 HELIX 3 3 VAL A 82 ARG A 91 1 10 HELIX 4 4 ASN A 99 LEU A 114 1 16 HELIX 5 5 LYS A 120 PHE A 124 5 5 HELIX 6 6 SER A 130 PHE A 138 1 9 HELIX 7 7 SER A 144 TYR A 152 1 9 HELIX 8 8 GLY A 163 THR A 179 1 17 HELIX 9 9 GLN B 10 ALA B 23 1 14 HELIX 10 10 GLY B 24 TYR B 31 5 8 HELIX 11 11 GLU B 38 GLN B 44 1 7 HELIX 12 12 PRO B 45 HIS B 47 5 3 HELIX 13 13 LEU B 48 LEU B 61 1 14 HELIX 14 14 LEU B 61 LEU B 66 1 6 SHEET 1 AA 2 ARG A 42 LEU A 43 0 SHEET 2 AA 2 ILE A 30 VAL A 39 1 O VAL A 39 N ARG A 42 SHEET 1 AB 2 PHE A 48 TYR A 51 0 SHEET 2 AB 2 ILE A 30 VAL A 39 -1 O ILE A 33 N VAL A 50 SHEET 1 AC 5 LYS A 126 ASP A 129 0 SHEET 2 AC 5 GLU A 94 ILE A 97 1 O LEU A 95 N THR A 128 SHEET 3 AC 5 GLN A 8 THR A 15 1 O ILE A 9 N VAL A 96 SHEET 4 AC 5 ILE A 30 VAL A 39 -1 N ILE A 31 O GLU A 14 SHEET 5 AC 5 ARG A 42 LEU A 43 1 O ARG A 42 N VAL A 39 SHEET 1 AD 5 LYS A 126 ASP A 129 0 SHEET 2 AD 5 GLU A 94 ILE A 97 1 O LEU A 95 N THR A 128 SHEET 3 AD 5 GLN A 8 THR A 15 1 O ILE A 9 N VAL A 96 SHEET 4 AD 5 ILE A 30 VAL A 39 -1 N ILE A 31 O GLU A 14 SHEET 5 AD 5 PHE A 48 TYR A 51 -1 O PHE A 48 N ALA A 35 LINK OD2 ASP A 12 CA CA A 190 1555 1555 1.74 LINK OD1 ASP A 12 CA CA A 190 1555 1555 2.92 LINK OE2 GLU A 14 CA CA A 190 1555 1555 1.74 LINK OD2 ASP A 167 CA CA A 190 1555 1555 1.74 SITE 1 AC1 3 ASP A 12 GLU A 14 ASP A 167 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