[English] 日本語
Yorodumi
- PDB-5tup: X-ray Crystal Structure of the Aspergillus fumigatus Sliding Clamp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tup
TitleX-ray Crystal Structure of the Aspergillus fumigatus Sliding Clamp
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / sliding clamp
Function / homology
Function and homology information


myosin binding / DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / membrane => GO:0016020 / DNA binding / nucleus
Similarity search - Function
Myosin-binding domain / Mysoin-binding motif of peroxisomes / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / 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 ...Myosin-binding domain / Mysoin-binding motif of peroxisomes / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / 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 speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.602 Å
AuthorsBruning, J.B. / Marshall, A.C. / Kroker, A.J. / Wegener, K.L. / Rajapaksha, H.
CitationJournal: FEBS J. / Year: 2017
Title: Structure of the sliding clamp from the fungal pathogen Aspergillus fumigatus (AfumPCNA) and interactions with Human p21.
Authors: Marshall, A.C. / Kroker, A.J. / Murray, L.A. / Gronthos, K. / Rajapaksha, H. / Wegener, K.L. / Bruning, J.B.
History
DepositionNov 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection
Category: diffrn_source / pdbx_struct_assembly_auth_evidence
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 4, 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
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)85,2223
Polymers85,2223
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.950, 103.370, 79.200
Angle α, β, γ (deg.)90.000, 96.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETchain AAA1 - 2542 - 255
2METMETchain BBB1 - 2542 - 255
3GLYGLYchain CCC0 - 2541 - 255
DetailsTrimer as determined by gel filtration

-
Components

#1: Protein Proliferating cell nuclear antigen


Mass: 28407.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_06803 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J5SJF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M KCl, 20 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 8, 2015 / Details: Si ans Rh coatings
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→78.68 Å / Num. obs: 27932 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 55.34 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.076 / Rrim(I) all: 0.204 / Net I/σ(I): 7.2 / Num. measured all: 197392 / Scaling rejects: 93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.6-2.726.62.01845540.33196.7
9.01-78.686.50.0650.995198.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.85 Å43.94 Å
Translation2.85 Å43.94 Å

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CS5

4cs5


Resolution: 2.602→44.024 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1375 4.94 %Random
Rwork0.196 ---
obs0.199 27806 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.32 Å2 / Biso mean: 73.7281 Å2 / Biso min: 28.49 Å2
Refinement stepCycle: final / Resolution: 2.602→44.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5613 0 0 183 5796
Biso mean---61.08 -
Num. residues----763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035686
X-RAY DIFFRACTIONf_angle_d0.7527728
X-RAY DIFFRACTIONf_chiral_restr0.026954
X-RAY DIFFRACTIONf_plane_restr0.004997
X-RAY DIFFRACTIONf_dihedral_angle_d10.1012032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3306X-RAY DIFFRACTION14.158TORSIONAL
12B3306X-RAY DIFFRACTION14.158TORSIONAL
13C3306X-RAY DIFFRACTION14.158TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.602-2.6950.34981470.30782489263694
2.695-2.80290.34391440.28382571271598
2.8029-2.93040.35781370.27052636277399
2.9304-3.08490.30321360.24326592795100
3.0849-3.27810.28721250.228226862811100
3.2781-3.53110.25471230.188226732796100
3.5311-3.88630.2731310.188926452776100
3.8863-4.44810.22851380.17326852823100
4.4481-5.60240.2151540.156326692823100
5.6024-44.03080.2361400.182427182858100
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)
15.1563-0.8966-1.33833.38011.63457.6196-0.03590.4448-0.0769-0.05790.0819-0.1978-0.07841.0663-0.05720.5403-0.13140.0510.5188-0.09190.419224.912625.619627.9051
27.0416-2.1867-0.34986.2984-0.43956.10490.47030.8989-0.2331-1.4434-0.2192-0.0326-0.51331.5027-0.27251.0176-0.15370.01770.9816-0.20630.386425.191323.796514.2897
30.24071.2294-0.97376.4671-5.96775.5189-0.44460.07370.70770.8431-0.7519-1.2568-1.40821.52281.08731.0411-0.26370.00460.7429-0.26420.89926.671431.697439.3969
47.3611-0.8506-1.26614.8567-0.07865.6636-0.4216-0.1053-0.26820.53360.21420.05420.29350.38710.20450.53160.02640.02360.2747-0.00690.401613.29248.498949.0996
55.98440.30260.41396.1372-1.77496.148-0.0312-0.04820.06130.35110.1586-0.16020.39740.8426-0.14230.45510.00720.03820.3396-0.06520.317420.608215.9445.1346
64.26882.4635-0.96134.3806-1.28087.2162-0.12570.26810.07340.28590.18410.14960.2491-0.1368-0.01150.53670.07320.0260.5066-0.00440.3567-11.07223.93810.0157
75.54911.2927-2.26912.00011.01452.34840.32990.70970.51910.38980.10920.5475-0.20050.4455-0.21550.64360.0267-0.04040.98220.05460.3697-11.33465.6738-0.2906
86.59212.77472.60982.44083.69738.31180.02380.4985-0.02820.49130.4145-0.7522-0.16130.7039-0.24780.8709-0.052-0.02710.59670.00230.465214.368721.97134.1734
98.90453.1651.39642.50570.30512.42980.57241.3291-1.4117-1.2642-0.3649-1.99210.38731.3024-0.66780.77110.02060.08910.9264-0.20241.064620.821911.7527-5.4854
107.65012.53311.75832.08113.05397.7343-0.09980.62120.25070.0210.00610.1007-0.07550.163-0.05160.5731-0.0735-0.01890.42690.08170.34284.640217.3909-2.148
116.64330.90864.03381.369-1.62516.9511-0.1783-0.1281-0.21050.1180.02780.1219-0.0932-0.62950.18550.85130.10230.040.3852-0.12230.4272-11.5542-2.386346.3444
127.45490.98423.43682.50391.01973.44110.2291-0.1282-0.1140.0799-0.0951-0.25390.28940.1991-0.11840.6590.04550.05070.3221-0.06420.3572-3.7436-2.135751.4205
136.83047.59594.61358.54275.44053.59090.0986-1.30621.32760.2479-1.031.6171-0.1581-0.84671.07680.79780.10720.26250.6189-0.06690.7669-24.2833-4.596747.001
144.4780.06090.56526.3199-1.6737.1990.14530.4602-0.0501-0.09590.07220.0102-0.08090.1739-0.18830.44380.09960.04730.3711-0.01310.2463-19.5731-8.323925.9386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 81 )A1 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 117 )A82 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 134 )A118 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 190 )A135 - 190
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 254 )A191 - 254
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 104 )B1 - 104
7X-RAY DIFFRACTION7chain 'B' and (resid 105 through 134 )B105 - 134
8X-RAY DIFFRACTION8chain 'B' and (resid 135 through 182 )B135 - 182
9X-RAY DIFFRACTION9chain 'B' and (resid 183 through 202 )B183 - 202
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 254 )B203 - 254
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 45 )C0 - 45
12X-RAY DIFFRACTION12chain 'C' and (resid 46 through 117 )C46 - 117
13X-RAY DIFFRACTION13chain 'C' and (resid 118 through 134 )C118 - 134
14X-RAY DIFFRACTION14chain 'C' and (resid 135 through 254 )C135 - 254

+
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