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- PDB-4yfu: Crystal structure of open Bacillus fragment DNA polymerase bound ... -

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Basic information

Entry
Database: PDB / ID: 4yfu
TitleCrystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP
Components
  • DNA polymerase
  • Primer DNA
  • Template DNA
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 / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
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 / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...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 / 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 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsWu, E.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Jeffress Trust United States
CitationJournal: Structure / Year: 2015
Title: The Closing Mechanism of DNA Polymerase I at Atomic Resolution.
Authors: Miller, B.R. / Beese, L.S. / Parish, C.A. / Wu, E.Y.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Refinement description
Revision 1.2Sep 16, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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_oper_list / struct_asym / struct_conn / 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 / _citation.journal_id_CSD / _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_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
D: DNA polymerase
B: Primer DNA
C: Template DNA
E: Primer DNA
F: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,91010
Polymers146,6476
Non-polymers1,2634
Water24,6991371
1
A: DNA polymerase
B: Primer DNA
C: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1485
Polymers73,3243
Non-polymers8242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-9 kcal/mol
Surface area27010 Å2
MethodPISA
2
D: DNA polymerase
E: Primer DNA
F: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7625
Polymers73,3243
Non-polymers4382
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-21 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.230, 108.100, 151.340
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 Primer DNA


Mass: 2714.811 Da / Num. of mol.: 2 / Fragment: Primer DNA oligonucleotide / Mutation: none / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Template DNA


Mass: 4329.830 Da / Num. of mol.: 2 / Fragment: Template DNA oligonucleotide / Mutation: none / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Sugars , 2 types, 4 molecules AD

#1: Protein DNA polymerase


Mass: 66279.062 Da / Num. of mol.: 2 / Fragment: DNA polymerase I, 5'-to-3' exonuclease-deficient / Mutation: D598A/F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1C9K5, 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 , 3 types, 1373 molecules

#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N2O14P3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1371 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: ~50% ammonium sulfate, MES pH 5.8, magnesium sulfate, methyl pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2007
RadiationMonochromator: Si111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44.7 Å / Num. obs: 241163 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.61 % / Biso Wilson estimate: 28.063 Å2 / Rmerge F obs: 0.079 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.071 / Χ2: 0.991 / Net I/σ(I): 13.33 / Num. measured all: 1111808
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.593.380.5580.4982.7912594238744372590.58496.2
1.59-1.70.2760.3365.1517821936897368900.377100
1.7-1.830.1540.1968.2216202432998329860.219100
1.83-2.010.0920.11912.0916063732756327200.13399.9
2.01-2.590.0470.06719.0626340453950538070.07599.7
2.59-3.170.0330.05324.5210510321676215790.0699.6
3.17-4.470.030.0527.27865216908167520.05799.1
4.470.0320.0526.5637827971491700.05894.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
REFMACphasing
Cootmodel building
RefinementResolution: 1.5→44.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2548 / WRfactor Rwork: 0.2152 / FOM work R set: 0.8326 / SU B: 1.589 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0755 / SU Rfree: 0.0796 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 11140 4.6 %RANDOM
Rwork0.195 ---
obs0.1966 230017 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.56 Å2 / Biso mean: 28.759 Å2 / Biso min: 4.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9307 836 118 1371 11632
Biso mean--28.98 39.05 -
Num. residues----1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01910669
X-RAY DIFFRACTIONr_angle_refined_deg2.5291.90814644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62524.224464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.335151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6061577
X-RAY DIFFRACTIONr_chiral_restr0.1660.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0217694
X-RAY DIFFRACTIONr_mcbond_it2.6742.4114683
X-RAY DIFFRACTIONr_mcangle_it3.4013.6075863
X-RAY DIFFRACTIONr_scbond_it4.4562.885986
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 836 -
Rwork0.292 15865 -
all-16701 -
obs--93.6 %

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