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- PDB-3px4: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -

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Basic information

Entry
Database: PDB / ID: 3px4
TitleCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation
Components
  • DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / TRANSFERASE-DNA complex / Cytosine-Adenine / closed conformation
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
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
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.582 Å
AuthorsWang, W. / Beese, L.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Authors: Wang, W. / Hellinga, H.W. / Beese, L.S.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.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_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,45211
Polymers148,3336
Non-polymers1,1195
Water26,4461468
1
A: DNA polymerase I
B: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
C: DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6184
Polymers74,1673
Non-polymers4511
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-21 kcal/mol
Surface area26580 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
F: DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8347
Polymers74,1673
Non-polymers6684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-36 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.680, 109.190, 150.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase I


Mass: 67490.289 Da / Num. of mol.: 2
Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment)
Mutation: D598A, F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')


Mass: 2635.751 Da / Num. of mol.: 2 / Fragment: DNA primer strand / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')


Mass: 4040.647 Da / Num. of mol.: 2 / Fragment: DNA template strand / Source method: obtained synthetically

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Non-polymers , 4 types, 1473 molecules

#4: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1468 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE. IT DIFFERS FROM UNP Q5KWC1 BY THIS SINGLE RESIDUE.

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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: 52.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Ammonium Sulfate, MPD, MgSO4, MES, pH 5.8, vapor diffusion, hanging drop, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2MPD11
3MgSO411
4MES11
5Ammonium Sulfate12
6MPD12
7MgSO412
8MES12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.58→100 Å / Num. all: 210662 / Num. obs: 200999 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 21.94
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.58-1.680.6012.4189.5
1.68-1.790.3684.7199.9
1.79-1.940.1918.5189.9
1.94-2.120.10914.2199.8
2.12-2.370.06223190.6
2.37-2.740.0436.1199.9
2.74-3.350.02848.1199.8
3.35-4.740.02358.9198.6
4.74-1000.0267197.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2HVI with insertion site base pair, metal ions, and protein residues 680-717 deleted

2hvi


Resolution: 1.582→71.099 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.47 / σ(F): 2.35 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 8581 4.56 %
Rwork0.2107 --
obs0.212 188106 89.64 %
all-210662 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.522 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4168 Å20 Å20 Å2
2--0.8279 Å2-0 Å2
3---0.5889 Å2
Refinement stepCycle: LAST / Resolution: 1.582→71.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9046 789 65 1468 11368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810201
X-RAY DIFFRACTIONf_angle_d1.16913968
X-RAY DIFFRACTIONf_dihedral_angle_d16.193937
X-RAY DIFFRACTIONf_chiral_restr0.0631560
X-RAY DIFFRACTIONf_plane_restr0.0061670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.582-1.60.33991860.29023542X-RAY DIFFRACTION54
1.6-1.61880.29152660.28545049X-RAY DIFFRACTION77
1.6188-1.63860.32192810.28295339X-RAY DIFFRACTION81
1.6386-1.65930.31842960.26525634X-RAY DIFFRACTION86
1.6593-1.68110.2913040.25455770X-RAY DIFFRACTION88
1.6811-1.70420.29633100.24355884X-RAY DIFFRACTION89
1.7042-1.72850.273090.23465897X-RAY DIFFRACTION90
1.7285-1.75430.2753160.23366011X-RAY DIFFRACTION91
1.7543-1.78170.25983180.23076028X-RAY DIFFRACTION92
1.7817-1.81090.26153210.21876111X-RAY DIFFRACTION93
1.8109-1.84220.25323240.21396145X-RAY DIFFRACTION92
1.8422-1.87570.263200.21366093X-RAY DIFFRACTION93
1.8757-1.91180.33462240.29944241X-RAY DIFFRACTION64
1.9118-1.95080.46592470.43624753X-RAY DIFFRACTION72
1.9508-1.99320.26772640.21076199X-RAY DIFFRACTION93
1.9932-2.03960.21762420.19496497X-RAY DIFFRACTION97
2.0396-2.09060.20492400.1956470X-RAY DIFFRACTION97
2.0906-2.14710.20312650.18596556X-RAY DIFFRACTION97
2.1471-2.21030.22552830.20076468X-RAY DIFFRACTION97
2.2103-2.28160.43091810.37574164X-RAY DIFFRACTION62
2.2816-2.36320.24442510.19136533X-RAY DIFFRACTION97
2.3632-2.45780.23392660.18586631X-RAY DIFFRACTION99
2.4578-2.56970.20912700.18946642X-RAY DIFFRACTION99
2.5697-2.70520.2132940.19596644X-RAY DIFFRACTION99
2.7052-2.87460.24332920.1996668X-RAY DIFFRACTION99
2.8746-3.09660.23233240.20146684X-RAY DIFFRACTION99
3.0966-3.40820.20193440.18866674X-RAY DIFFRACTION99
3.4082-3.90140.20233320.18156555X-RAY DIFFRACTION97
3.9014-4.91510.19473540.16336762X-RAY DIFFRACTION99
4.9151-71.17050.22333570.21386881X-RAY DIFFRACTION98

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