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- PDB-1xwl: BACILLUS STEAROTHERMOPHILUS (NEWLY IDENTIFIED STRAIN AS YET UNNAM... -

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Basic information

Entry
Database: PDB / ID: 1xwl
TitleBACILLUS STEAROTHERMOPHILUS (NEWLY IDENTIFIED STRAIN AS YET UNNAMED) DNA POLYMERASE FRAGMENT
ComponentsDNA POLYMERASE I
KeywordsDNA REPLICATION / BACILLUS STEAROTHERMOPHILUS DNA POLYMERASE / BF THERMOPHILUS POLYMERASE
Function / homology
Function and homology information


5'-3' exonuclease activity / 3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKiefer, J.R. / Mao, C. / Beese, L.S.
Citation
Journal: Structure / Year: 1997
Title: Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
Authors: Kiefer, J.R. / Mao, C. / Hansen, C.J. / Basehore, S.L. / Hogrefe, H.H. / Braman, J.C. / Beese, L.S.
#1: Journal: Nature / Year: 1998
Title: Visualizing DNA Replication in a Catalytically Active Bacillus DNA Polymerase Crystal
Authors: Kiefer, J.R. / Mao, C. / Braman, J.C. / Beese, L.S.
History
DepositionJul 22, 1998Processing site: BNL
SupersessionJan 13, 1999ID: 1BDP
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3653
Polymers66,1731
Non-polymers1922
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.106, 93.868, 104.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA POLYMERASE I / BF


Mass: 66172.844 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: BACILLUS STEAROTHERMOPHILUS / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Production host: Escherichia coli (E. coli) / References: UniProt: P52026, DNA-directed DNA polymerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBACILLUS FRAGMENT (BF) IS THE C-TERMINAL 592 AMINO ACIDS OF THE WILD TYPE BACILLUS DNA POLYMERASE. ...BACILLUS FRAGMENT (BF) IS THE C-TERMINAL 592 AMINO ACIDS OF THE WILD TYPE BACILLUS DNA POLYMERASE. THIS POLYMERASE RETAINS POLYMERASE ACTIVITY BUT LACKS ALL EXONUCLEASE ACTIVITY. BF IS A THERMOSTABLE ENZYME AND HAS AN OPTIMAL TEMPERATURE FOR ACTIVITY OF 65 DEGREES CELSIUS. THE PROTEIN IS HOMOLOGOUS TO ESCHERICHIA COLI DNA POLYMERASE I AND THERMUS AQUATICUS (TAQ) DNA POLYMERASE. THE SECONDARY STRUCTURAL ELEMENTS OF THE ENZYME HAVE BEEN ASSIGNED USING THE KABSCH AND SANDER ALGORITHM ENCODED IN PROCHECK AND THEN WERE NAMED TO BE CONSISTENT WITH THE STRUCTURE OF THE KLENOW FRAGMENT (KF) OF ESCHERICHIA COLI DNA POLYMERASE I. IN THE FOLLOWING TOPOLOGY ASSIGNMENT, HELICES ARE INDICATED AS CAPITAL LETTERS AND SHEETS ARE REPRESENTED BY NUMBERS. THE RESIDUE RANGE COVERED BY THE SECONDARY STRUCTURE ELEMENT IS SHOWN IN PARENTHESES. LETTERS AND NUMBERS FOLLOWING THE INITIAL LETTERS INDICATE ELEMENTS FOUND IN THE REFINED KF STRUCTURES OR ONLY IN THIS STRUCTURE. VESTIGIAL EXONUCLEASE DOMAIN: 1 (302 - 304), A (308 - 312), 2 (314 - 321), 3 (334 - 339), 4 (342 - 346), A1 (347 - 353), B (354 - 363), 5 (367 - 370), C (372 - 382), 5A (389 - 393), D (394 - 402), E(409-416), E1 (424 - 430), F (439 - 468); POLYMERASE DOMAIN: G (470 - 477), G1 (478 - 492), 6 (493 - 495), H (496 - 522), H1 (530 - 540), H2 (557 - 565), I (568 - 588), I1 (589 - 595), 6A (600 - 602), 7 (605 - 607), 8 (617 - 619), J (622 - 626), K (633 - 638), 8A (639 - 641), 9 (646 - 655), L (656 - 667), M (668 - 677), N (680 - 691), N1 (693 - 697), O (698 - 714), O1 (717 - 726), O2 (728 - 743), P (744 - 761), 10 (762 - 765), 11 (769 - 773), P1 (774 - 778), Q (780 - 818), 12 (823 - 828), 13 (830 - 838), R (840 - 854), 14 (863 - 869), S (871 - 876)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 62 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal
*PLUS
Density % sol: 63.4 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
255 %(v/v)satammonium sulfate1reservoir
3100 mMMES1reservoir
42.5-7.0 %(v/v)MPD1reservoir
50.02 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 90 K
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 89072 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.038 / Net I/σ(I): 16.2
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.182 / % possible all: 83.1
Reflection
*PLUS
Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 83.1 % / Rmerge(I) obs: 0.182

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ORIGINAL 1BDP COORDINATES

1bdp
PDB Unreleased entry


Resolution: 1.7→20 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 4491 5 %RANDOM
Rwork0.254 ---
obs0.254 89018 89.3 %-
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-20 Å
Luzzati sigma a-0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 10 405 5069
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.951.5
X-RAY DIFFRACTIONx_mcangle_it1.582
X-RAY DIFFRACTIONx_scbond_it1.852
X-RAY DIFFRACTIONx_scangle_it3.052.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.424 663 5.1 %
Rwork0.422 12305 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM_SULFATE.TXTTOP_SULFATE.TXT
X-RAY DIFFRACTION4PARAMETER.ELEMENTS

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