HEADER DNA BINDING PROTEIN 06-APR-23 8OOY TITLE POL I BOUND TO EXTENDED AND DISPLACED DNA SECTION - OPEN CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL I; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TEMPLATE DNA; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: EXTENDING PRIMER; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DISPLACING PRIMER; COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 3 ORGANISM_TAXID: 866768; SOURCE 4 GENE: POLA, RESA, B3863, JW3835; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE I, OKAZAKI FRAGMENT MATURATION, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.BOTTO,A.BORSELLINI,M.H.LAMERS REVDAT 3 01-NOV-23 8OOY 1 JRNL REVDAT 2 06-SEP-23 8OOY 1 JRNL REVDAT 1 09-AUG-23 8OOY 0 JRNL AUTH M.M.BOTTO,A.BORSELLINI,M.H.LAMERS JRNL TITL A FOUR-POINT MOLECULAR HANDOVER DURING OKAZAKI MATURATION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 1505 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 37620586 JRNL DOI 10.1038/S41594-023-01071-Y REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 REMARK 3 NUMBER OF PARTICLES : 164102 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8OOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292129461. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : ESCHERICHIA COLI DNA POLYMERASE REMARK 245 I IN COMPLEX WITH DNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 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 A T 11 O2' REMARK 470 A T 12 O2' REMARK 470 C T 13 O2' REMARK 470 G T 14 O2' REMARK 470 C T 16 O2' REMARK 470 G T 17 O2' REMARK 470 G T 19 O2' REMARK 470 A T 20 O2' REMARK 470 C T 21 O2' REMARK 470 G T 23 O2' REMARK 470 G T 24 O2' REMARK 470 G T 25 O2' REMARK 470 A T 26 O2' REMARK 470 A T 27 O2' REMARK 470 A T 28 O2' REMARK 470 A T 29 O2' REMARK 470 C T 30 O2' REMARK 470 C T 31 O2' REMARK 470 C T 32 O2' REMARK 470 G T 34 O2' REMARK 470 G T 35 O2' REMARK 470 C T 36 O2' REMARK 470 G P 1 O2' REMARK 470 C P 2 O2' REMARK 470 C P 3 O2' REMARK 470 A P 4 O2' REMARK 470 G P 5 O2' REMARK 470 G P 6 O2' REMARK 470 G P 7 O2' REMARK 470 C P 12 O2' REMARK 470 C P 13 O2' REMARK 470 C P 14 O2' REMARK 470 A P 15 O2' REMARK 470 G P 16 O2' REMARK 470 C P 18 O2' 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 328 -5.99 72.17 REMARK 500 ASN A 329 54.29 -97.25 REMARK 500 ALA A 374 51.11 -140.26 REMARK 500 VAL A 663 -47.25 -138.70 REMARK 500 ASP A 673 73.16 53.03 REMARK 500 GLU A 697 137.27 -170.96 REMARK 500 ASP A 698 18.25 56.91 REMARK 500 ASP A 882 50.32 35.80 REMARK 500 SER A 920 31.24 -140.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17033 RELATED DB: EMDB REMARK 900 POL I BOUND TO EXTENDED AND DISPLACED DNA SECTION - OPEN REMARK 900 CONFORMATION DBREF 8OOY A 328 928 UNP P00582 DPO1_ECOLI 328 928 DBREF 8OOY T 11 36 PDB 8OOY 8OOY 11 36 DBREF 8OOY P 1 18 PDB 8OOY 8OOY 1 18 DBREF 8OOY D 8 14 PDB 8OOY 8OOY 8 14 SEQADV 8OOY GLY A 325 UNP P00582 EXPRESSION TAG SEQADV 8OOY PRO A 326 UNP P00582 EXPRESSION TAG SEQADV 8OOY HIS A 327 UNP P00582 EXPRESSION TAG SEQRES 1 A 604 GLY PRO HIS ASP ASN TYR VAL THR ILE LEU ASP GLU GLU SEQRES 2 A 604 THR LEU LYS ALA TRP ILE ALA LYS LEU GLU LYS ALA PRO SEQRES 3 A 604 VAL PHE ALA PHE ASP THR GLU THR ASP SER LEU ASP ASN SEQRES 4 A 604 ILE SER ALA ASN LEU VAL GLY LEU SER PHE ALA ILE GLU SEQRES 5 A 604 PRO GLY VAL ALA ALA TYR ILE PRO VAL ALA HIS ASP TYR SEQRES 6 A 604 LEU ASP ALA PRO ASP GLN ILE SER ARG GLU ARG ALA LEU SEQRES 7 A 604 GLU LEU LEU LYS PRO LEU LEU GLU ASP GLU LYS ALA LEU SEQRES 8 A 604 LYS VAL GLY GLN ASN LEU LYS TYR ASP ARG GLY ILE LEU SEQRES 9 A 604 ALA ASN TYR GLY ILE GLU LEU ARG GLY ILE ALA PHE ASP SEQRES 10 A 604 THR MET LEU GLU SER TYR ILE LEU ASN SER VAL ALA GLY SEQRES 11 A 604 ARG HIS ASP MET ASP SER LEU ALA GLU ARG TRP LEU LYS SEQRES 12 A 604 HIS LYS THR ILE THR PHE GLU GLU ILE ALA GLY LYS GLY SEQRES 13 A 604 LYS ASN GLN LEU THR PHE ASN GLN ILE ALA LEU GLU GLU SEQRES 14 A 604 ALA GLY ARG TYR ALA ALA GLU ASP ALA ASP VAL THR LEU SEQRES 15 A 604 GLN LEU HIS LEU LYS MET TRP PRO ASP LEU GLN LYS HIS SEQRES 16 A 604 LYS GLY PRO LEU ASN VAL PHE GLU ASN ILE GLU MET PRO SEQRES 17 A 604 LEU VAL PRO VAL LEU SER ARG ILE GLU ARG ASN GLY VAL SEQRES 18 A 604 LYS ILE ASP PRO LYS VAL LEU HIS ASN HIS SER GLU GLU SEQRES 19 A 604 LEU THR LEU ARG LEU ALA GLU LEU GLU LYS LYS ALA HIS SEQRES 20 A 604 GLU ILE ALA GLY GLU GLU PHE ASN LEU SER SER THR LYS SEQRES 21 A 604 GLN LEU GLN THR ILE LEU PHE GLU LYS GLN GLY ILE LYS SEQRES 22 A 604 PRO LEU LYS LYS THR PRO GLY GLY ALA PRO SER THR SER SEQRES 23 A 604 GLU GLU VAL LEU GLU GLU LEU ALA LEU ASP TYR PRO LEU SEQRES 24 A 604 PRO LYS VAL ILE LEU GLU TYR ARG GLY LEU ALA LYS LEU SEQRES 25 A 604 LYS SER THR TYR THR ASP LYS LEU PRO LEU MET ILE ASN SEQRES 26 A 604 PRO LYS THR GLY ARG VAL HIS THR SER TYR HIS GLN ALA SEQRES 27 A 604 VAL THR ALA THR GLY ARG LEU SER SER THR ASP PRO ASN SEQRES 28 A 604 LEU GLN ASN ILE PRO VAL ARG ASN GLU GLU GLY ARG ARG SEQRES 29 A 604 ILE ARG GLN ALA PHE ILE ALA PRO GLU ASP TYR VAL ILE SEQRES 30 A 604 VAL SER ALA ASP TYR SER GLN ILE GLU LEU ARG ILE MET SEQRES 31 A 604 ALA HIS LEU SER ARG ASP LYS GLY LEU LEU THR ALA PHE SEQRES 32 A 604 ALA GLU GLY LYS ASP ILE HIS ARG ALA THR ALA ALA GLU SEQRES 33 A 604 VAL PHE GLY LEU PRO LEU GLU THR VAL THR SER GLU GLN SEQRES 34 A 604 ARG ARG SER ALA LYS ALA ILE ASN PHE GLY LEU ILE TYR SEQRES 35 A 604 GLY MET SER ALA PHE GLY LEU ALA ARG GLN LEU ASN ILE SEQRES 36 A 604 PRO ARG LYS GLU ALA GLN LYS TYR MET ASP LEU TYR PHE SEQRES 37 A 604 GLU ARG TYR PRO GLY VAL LEU GLU TYR MET GLU ARG THR SEQRES 38 A 604 ARG ALA GLN ALA LYS GLU GLN GLY TYR VAL GLU THR LEU SEQRES 39 A 604 ASP GLY ARG ARG LEU TYR LEU PRO ASP ILE LYS SER SER SEQRES 40 A 604 ASN GLY ALA ARG ARG ALA ALA ALA GLU ARG ALA ALA ILE SEQRES 41 A 604 ASN ALA PRO MET GLN GLY THR ALA ALA ASP ILE ILE LYS SEQRES 42 A 604 ARG ALA MET ILE ALA VAL ASP ALA TRP LEU GLN ALA GLU SEQRES 43 A 604 GLN PRO ARG VAL ARG MET ILE MET GLN VAL HIS ASP GLU SEQRES 44 A 604 LEU VAL PHE GLU VAL HIS LYS ASP ASP VAL ASP ALA VAL SEQRES 45 A 604 ALA LYS GLN ILE HIS GLN LEU MET GLU ASN CYS THR ARG SEQRES 46 A 604 LEU ASP VAL PRO LEU LEU VAL GLU VAL GLY SER GLY GLU SEQRES 47 A 604 ASN TRP ASP GLN ALA HIS SEQRES 1 T 26 A A C G DT C G DT G A C DT G SEQRES 2 T 26 G G A A A A C C C DT G G C SEQRES 1 P 18 G C C A G G G DT DT DT DT C C SEQRES 2 P 18 C A G DT C SEQRES 1 D 7 DC DG DA DC DG DT DT HET MG A1001 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG MG 2+ HELIX 1 AA1 ASP A 335 LYS A 348 1 14 HELIX 2 AA2 SER A 397 GLU A 410 1 14 HELIX 3 AA3 ASN A 420 ASN A 430 1 11 HELIX 4 AA4 THR A 442 ASN A 450 1 9 HELIX 5 AA5 ASP A 457 LEU A 466 1 10 HELIX 6 AA6 THR A 472 GLY A 478 1 7 HELIX 7 AA7 THR A 485 ILE A 489 5 5 HELIX 8 AA8 ALA A 490 HIS A 519 1 30 HELIX 9 AA9 HIS A 519 ILE A 529 1 11 HELIX 10 AB1 PRO A 532 GLY A 544 1 13 HELIX 11 AB2 ASP A 548 GLY A 575 1 28 HELIX 12 AB3 SER A 582 GLN A 594 1 13 HELIX 13 AB4 SER A 610 LEU A 619 1 10 HELIX 14 AB5 TYR A 621 TYR A 640 1 20 HELIX 15 AB6 ASP A 642 MET A 647 1 6 HELIX 16 AB7 ASN A 675 ILE A 679 5 5 HELIX 17 AB8 ASN A 683 ALA A 692 1 10 HELIX 18 AB9 GLN A 708 ARG A 719 1 12 HELIX 19 AC1 ASP A 720 GLY A 730 1 11 HELIX 20 AC2 ASP A 732 GLY A 743 1 12 HELIX 21 AC3 PRO A 745 VAL A 749 5 5 HELIX 22 AC4 THR A 750 GLY A 767 1 18 HELIX 23 AC5 SER A 769 ASN A 778 1 10 HELIX 24 AC6 PRO A 780 TYR A 795 1 16 HELIX 25 AC7 TYR A 795 GLN A 812 1 18 HELIX 26 AC8 ASN A 832 GLN A 871 1 40 HELIX 27 AC9 ASP A 892 ASN A 906 1 15 HELIX 28 AD1 ASN A 923 HIS A 928 1 6 SHEET 1 AA1 4 TYR A 330 THR A 332 0 SHEET 2 AA1 4 VAL A 379 PRO A 384 1 O ALA A 380 N VAL A 331 SHEET 3 AA1 4 LEU A 368 GLU A 376 -1 N PHE A 373 O ALA A 381 SHEET 4 AA1 4 GLU A 357 THR A 358 -1 N GLU A 357 O GLY A 370 SHEET 1 AA2 3 VAL A 351 ALA A 353 0 SHEET 2 AA2 3 LEU A 415 GLY A 418 1 O VAL A 417 N PHE A 352 SHEET 3 AA2 3 ILE A 438 ASP A 441 1 O PHE A 440 N LYS A 416 SHEET 1 AA3 2 SER A 658 HIS A 660 0 SHEET 2 AA3 2 SER A 670 THR A 672 -1 O THR A 672 N SER A 658 SHEET 1 AA4 2 TYR A 699 VAL A 702 0 SHEET 2 AA4 2 PHE A 886 HIS A 889 -1 O PHE A 886 N VAL A 702 LINK OD1 ASP A 355 MG MG A1001 1555 1555 2.02 CISPEP 1 ASP A 673 PRO A 674 0 -6.85 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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