[English] 日本語
Yorodumi
- PDB-5hac: Crystal structure of Proliferating Cell Nuclear Antigen from Leis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hac
TitleCrystal structure of Proliferating Cell Nuclear Antigen from Leishmania donovani at 2.95 A 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
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSingh, P.K. / Yadav, S.P. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of Proliferating Cell Nuclear Antigen from Leishmania donovani at 2.95 A resolution
Authors: Singh, P.K. / Yadav, S.P. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)197,9486
Polymers197,9486
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-30 kcal/mol
Surface area70900 Å2
Unit cell
Length a, b, c (Å)133.992, 150.185, 170.079
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
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVALAA-6 - 2882 - 296
21LEULEUVALVALBB-6 - 2882 - 296
12LEULEUASPASPAA-6 - 2892 - 297
22LEULEUASPASPCC-6 - 2892 - 297
13LEULEUVALVALAA-6 - 2882 - 296
23LEULEUVALVALDD-6 - 2882 - 296
14VALVALVALVALAA-5 - 2883 - 296
24VALVALVALVALEE-5 - 2883 - 296
15LEULEUVALVALAA-6 - 2882 - 296
25LEULEUVALVALFF-6 - 2882 - 296
16LEULEUVALVALBB-6 - 2882 - 296
26LEULEUVALVALCC-6 - 2882 - 296
17GLYGLYASPASPBB-7 - 2891 - 297
27GLYGLYASPASPDD-7 - 2891 - 297
18VALVALVALVALBB-5 - 2883 - 296
28VALVALVALVALEE-5 - 2883 - 296
19GLYGLYASPASPBB-7 - 2891 - 297
29GLYGLYASPASPFF-7 - 2891 - 297
110LEULEUVALVALCC-6 - 2882 - 296
210LEULEUVALVALDD-6 - 2882 - 296
111VALVALVALVALCC-5 - 2883 - 296
211VALVALVALVALEE-5 - 2883 - 296
112LEULEUVALVALCC-6 - 2882 - 296
212LEULEUVALVALFF-6 - 2882 - 296
113VALVALVALVALDD-5 - 2883 - 296
213VALVALVALVALEE-5 - 2883 - 296
114GLYGLYASPASPDD-7 - 2891 - 297
214GLYGLYASPASPFF-7 - 2891 - 297
115VALVALVALVALEE-5 - 2883 - 296
215VALVALVALVALFF-5 - 2883 - 296

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: 32991.281 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: PCNA / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: B5TV91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.32 Å3/Da / Density % sol: 74.7 % / Description: RECTANGULAR
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, SODIUM MALONATE / PH range: 4.5- 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 64552 / % possible obs: 76.3 % / Redundancy: 5.5 % / Net I/σ(I): 14.2
Reflection shellResolution: 2.95→2.96 Å / Mean I/σ(I) obs: 0.6 / % possible all: 86.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CFK

5cfk


Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 17.767 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.562 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23234 966 1.5 %RANDOM
Rwork0.20457 ---
obs0.20501 63541 88.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.249 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å2-0 Å20 Å2
2--0.99 Å20 Å2
3----3.74 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12052 0 0 24 12076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01912238
X-RAY DIFFRACTIONr_bond_other_d0.010.0211740
X-RAY DIFFRACTIONr_angle_refined_deg2.2911.97316516
X-RAY DIFFRACTIONr_angle_other_deg1.944327056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.51651550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59524.607534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.855152200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5191572
X-RAY DIFFRACTIONr_chiral_restr0.1170.21906
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213790
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022666
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_it9.66210.2796236
X-RAY DIFFRACTIONr_mcbond_other9.66210.2786235
X-RAY DIFFRACTIONr_mcangle_it14.45915.3977774
X-RAY DIFFRACTIONr_mcangle_other14.45915.3987775
X-RAY DIFFRACTIONr_scbond_it11.20311.0566002
X-RAY DIFFRACTIONr_scbond_other11.20111.0556000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.98516.2348742
X-RAY DIFFRACTIONr_long_range_B_refined20.97278.99912943
X-RAY DIFFRACTIONr_long_range_B_other20.97378.99212942
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)
11A287140.12
12B287140.12
21A290120.12
22C290120.12
31A287560.12
32D287560.12
41A288140.12
42E288140.12
51A285080.13
52F285080.13
61B293260.1
62C293260.1
71B289000.11
72D289000.11
81B287240.12
82E287240.12
91B292100.12
92F292100.12
101C288400.11
102D288400.11
111C289120.11
112E289120.11
121C291180.12
122F291180.12
131D293940.11
132E293940.11
141D285840.12
142F285840.12
151E285160.12
152F285160.12
LS refinement shellResolution: 2.948→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 65 -
Rwork0.378 4333 -
obs--82.64 %

+
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