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- PDB-3ez5: Cocrystal structure of Bacillus fragment DNA polymerase I with du... -

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Basic information

Entry
Database: PDB / ID: 3ez5
TitleCocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).
Components
  • 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3'
  • 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / protein-DNA complex / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 ...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 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / 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
sucrose / 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsWarren, J.J. / Wu, E.Y. / Golosov, A.A. / Karplus, M. / Beese, L.S.
CitationJournal: Structure / Year: 2010
Title: The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis.
Authors: Golosov, A.A. / Warren, J.J. / Beese, L.S. / Karplus, M.
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I
D: DNA polymerase I
B: 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'
C: 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3'
E: 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'
F: 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,44418
Polymers145,1946
Non-polymers2,25012
Water9,728540
1
A: DNA polymerase I
B: 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'
C: 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7389
Polymers72,5973
Non-polymers1,1406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-115 kcal/mol
Surface area27310 Å2
MethodPISA
2
D: DNA polymerase I
E: 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'
F: 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7079
Polymers72,5973
Non-polymers1,1106
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-133 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.551, 108.572, 149.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'


Mass: 2691.774 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA primer strand
#3: DNA chain 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3'


Mass: 3702.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand

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Protein / Sugars , 2 types, 4 molecules AD

#1: Protein DNA polymerase I


Mass: 66202.945 Da / Num. of mol.: 2 / Mutation: F710Y
Source method: isolated from a genetically manipulated source
Details: The enzyme comes from a bacterium isolated from an Idaho hot spring, which was identified as a strain of Bacillus stearothermophilus by 16S rRNA sequence analysis (Kiefer, J.R. et al., 1997 Structure 5:95-108).
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: POLA / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P52026*PLUS, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 550 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-DAD / 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE


Mass: 475.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O11P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium Sulfate, MES, MPD, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2MES11
3MPD11
4Ammonium Sulfate12
5MSE12
6MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.28242 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28242 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 119138 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.78 % / Biso Wilson estimate: 39.668 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.28
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 121167 / Num. unique all: 121167 / Num. unique obs: 32718 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementStarting model: PDB ENTRY 2HVI

2hvi


Resolution: 1.9→46.83 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.278 / WRfactor Rwork: 0.235 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.83 / SU B: 3.672 / SU ML: 0.109 / SU R Cruickshank DPI: 0.159 / SU Rfree: 0.145 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.159 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5010 4.2 %RANDOM in 1.98-1.90 shell, inherited from 2HVI data set in 50-1.98 shell
Rwork0.211 ---
obs0.212 119138 99.97 %-
all-119174 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.23 Å2 / Biso mean: 37.225 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.145 Å0.159 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9312 846 124 540 10822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210550
X-RAY DIFFRACTIONr_angle_refined_deg1.3822.0914458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24651161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00124.174460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.694151754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6271577
X-RAY DIFFRACTIONr_chiral_restr0.0880.21623
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217595
X-RAY DIFFRACTIONr_mcbond_it0.7291.55797
X-RAY DIFFRACTIONr_mcangle_it1.38829351
X-RAY DIFFRACTIONr_scbond_it2.12634753
X-RAY DIFFRACTIONr_scangle_it3.4384.55105
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 435 -
Rwork0.273 8251 -
all-8686 -
obs-8686 100 %

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