[English] 日本語
Yorodumi
- PDB-5h0t: Crystal structure of proliferating cell nuclear antigen from Leis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h0t
TitleCrystal structure of proliferating cell nuclear antigen from Leishmania donovani at 2.73 Angstrom resolution
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


PCNA complex / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA binding
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsSingh, P.K. / Yadav, S.P. / Sharma, P.S. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Structure and binding studies of proliferating cell nuclear antigen from Leishmania donovani.
Authors: Yadav, S.P. / Singh, P.K. / Sharma, P. / Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_prerelease_seq
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,3248
Polymers193,1126
Non-polymers2122
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.800, 149.574, 169.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22E
13A
23B
14A
24C
15A
25F
16D
26E
17D
27B
18D
28C
19D
29F
110E
210B
111E
211C
112E
212F
113B
213C
114B
214F
115C
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 1 - 289 / Label seq-ID: 1 - 289

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21DB
12AA
22EC
13AA
23BD
14AA
24CE
15AA
25FF
16DB
26EC
17DB
27BD
18DB
28CE
19DB
29FF
110EC
210BD
111EC
211CE
112EC
212FF
113BD
213CE
114BD
214FF
115CE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Proliferating cell nuclear antigen


Mass: 32185.354 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: B5TV91
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 4.38 Å3/Da / Density % sol: 76.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG 3350, sodium malonate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 28, 2016 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.73→112.08 Å / Num. obs: 89366 / % possible obs: 90.7 % / Redundancy: 2.9 % / Net I/σ(I): 12
Reflection shellResolution: 2.73→2.78 Å / Mean I/σ(I) obs: 1.45 / % possible all: 80

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B7O

5b7o
PDB Unreleased entry


Resolution: 2.73→112.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.981 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23915 927 1 %RANDOM
Rwork0.19742 ---
obs0.19783 89366 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.614 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2--0.89 Å2-0 Å2
3----2.8 Å2
Refinement stepCycle: 1 / Resolution: 2.73→112.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11514 0 14 250 11778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911694
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211232
X-RAY DIFFRACTIONr_angle_refined_deg2.2961.97415772
X-RAY DIFFRACTIONr_angle_other_deg1.214325896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53251476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79324.941510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.107152118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6291560
X-RAY DIFFRACTIONr_chiral_restr0.1540.21830
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213146
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022526
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.3148.7725940
X-RAY DIFFRACTIONr_mcbond_other9.3138.775939
X-RAY DIFFRACTIONr_mcangle_it12.95113.1627404
X-RAY DIFFRACTIONr_mcangle_other12.95113.1647405
X-RAY DIFFRACTIONr_scbond_it11.1189.7665754
X-RAY DIFFRACTIONr_scbond_other11.1189.7665754
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.80314.2568369
X-RAY DIFFRACTIONr_long_range_B_refined19.39546737
X-RAY DIFFRACTIONr_long_range_B_other19.39546737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A148080.1
12D148080.1
21A147980.1
22E147980.1
31A148000.1
32B148000.1
41A145660.11
42C145660.11
51A145560.12
52F145560.12
61D147880.1
62E147880.1
71D148640.1
72B148640.1
81D146300.12
82C146300.12
91D145800.12
92F145800.12
101E145820.12
102B145820.12
111E146800.12
112C146800.12
121E146480.12
122F146480.12
131B147160.11
132C147160.11
141B145900.12
142F145900.12
151C147260.12
152F147260.12
LS refinement shellResolution: 2.728→2.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 57 -
Rwork0.387 6004 -
obs--91.29 %

+
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://pdbjlvh1.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