[English] 日本語
Yorodumi
- PDB-4p4m: Crystal structure of Leishmania infantum polymerase beta: Ternary... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p4m
TitleCrystal structure of Leishmania infantum polymerase beta: Ternary P/T complex
Components
  • DNA (5'-D(*CP*AP*GP*TP*A)-3')
  • DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / nucleus / metal ion binding
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9185 Å
AuthorsMejia, E. / Burak, M. / Alonso, A. / Larraga, V. / Kunkel, T.A. / Bebenek, K. / Garcia-Diaz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100021-02 United States
CitationJournal: DNA Repair (Amst.) / Year: 2014
Title: Structures of the Leishmania infantum polymerase beta.
Authors: Mejia, E. / Burak, M. / Alonso, A. / Larraga, V. / Kunkel, T.A. / Bebenek, K. / Garcia-Diaz, M.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase beta
D: DNA (5'-D(*CP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7886
Polymers46,2753
Non-polymers5133
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-32 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.680, 108.680, 151.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21A-555-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 42962.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6N3

-
DNA chain , 2 types, 2 molecules DE

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


Mass: 1504.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3')


Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 329 molecules

#4: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 120 mM magnesium chloride, 0.4 M Tris-HCl, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.918→94.13 Å / Num. obs: 41119 / % possible obs: 100 % / Redundancy: 18.7 % / Net I/σ(I): 38.4
Reflection shellResolution: 1.918→1.948 Å / % possible obs: 100 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.613 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
CBASSdata collection
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BPY

1bpy


Resolution: 1.9185→44.945 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 3100 7.55 %
Rwork0.1639 --
obs0.1653 41054 99.95 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9185→44.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 224 30 326 2682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142502
X-RAY DIFFRACTIONf_angle_d1.2923443
X-RAY DIFFRACTIONf_dihedral_angle_d15.647984
X-RAY DIFFRACTIONf_chiral_restr0.071377
X-RAY DIFFRACTIONf_plane_restr0.004410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9185-1.94850.23291360.18661663X-RAY DIFFRACTION99
1.9485-1.98040.19631370.17381689X-RAY DIFFRACTION100
1.9804-2.01460.17671390.16811698X-RAY DIFFRACTION100
2.0146-2.05120.16971390.17031704X-RAY DIFFRACTION100
2.0512-2.09070.18031380.16141689X-RAY DIFFRACTION100
2.0907-2.13330.18271380.1571687X-RAY DIFFRACTION100
2.1333-2.17970.17891390.16361697X-RAY DIFFRACTION100
2.1797-2.23040.1881380.16851692X-RAY DIFFRACTION100
2.2304-2.28620.25331390.16971700X-RAY DIFFRACTION100
2.2862-2.3480.18521400.17161714X-RAY DIFFRACTION100
2.348-2.41710.21451400.17241718X-RAY DIFFRACTION100
2.4171-2.49510.1951390.16631695X-RAY DIFFRACTION100
2.4951-2.58430.19521400.16561719X-RAY DIFFRACTION100
2.5843-2.68770.18621410.17391715X-RAY DIFFRACTION100
2.6877-2.810.1921400.16811719X-RAY DIFFRACTION100
2.81-2.95820.17021410.16781728X-RAY DIFFRACTION100
2.9582-3.14350.20811420.16611725X-RAY DIFFRACTION100
3.1435-3.38610.17461430.15751755X-RAY DIFFRACTION100
3.3861-3.72670.14471420.1451751X-RAY DIFFRACTION100
3.7267-4.26560.1261450.13231768X-RAY DIFFRACTION100
4.2656-5.37280.16611470.15291801X-RAY DIFFRACTION100
5.3728-44.95760.22471570.20271927X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.37841.17690.51376.37541.71713.31110.0328-1.13520.42230.70950.2619-0.1683-0.26120.5529-0.28470.3564-0.03770.01690.7602-0.18750.3717-3.9517-19.682511.4984
22.0873-0.7152-0.59810.88910.26581.31520.0541-0.0730.01150.0529-0.04040.092-0.1111-0.0659-0.01780.18670.0050.04150.119-0.00710.1554-8.497-34.1001-9.3048
32.5706-0.0381-1.29564.148-1.2633.0684-0.0007-0.1543-0.06060.2341-0.0281-0.28470.0550.27550.01010.16690.0318-0.02370.1589-0.0040.150311.0457-46.3236-9.5346
45.8851-3.6715-4.1886.1217-1.37247.12470.2817-1.03690.13440.0312-0.18970.0503-0.18890.2821-0.08950.241-0.0736-0.03980.41940.02070.26383.01-26.68030.4207
52.8841-1.10870.16054.3128-0.51592.42920.0794-0.23180.39670.3135-0.0138-0.2167-0.27510.1655-0.0750.2197-0.04360.04020.2032-0.02220.21956.7601-31.481-5.0266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 90 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 376 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 5 )
5X-RAY DIFFRACTION5chain 'E' and (resid 6 through 11 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more