[English] 日本語
Yorodumi
- PDB-3i2m: The Crystal Structure of PF-8, the DNA Polymerase Accessory Subun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i2m
TitleThe Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi s Sarcoma-Associated Herpesvirus
ComponentsORF59
KeywordsREPLICATION / processivity
Function / homologyDNA polymerase processivity factor, herpesviridae / Herpes DNA replication accessory factor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Alpha Beta / Core gene UL42 family protein
Function and homology information
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsBaltz, J.L. / Filman, D.J. / Ciustea, M. / Silverman, J.E.Y. / Lautenschlager, C.L. / Coen, D.M. / Ricciardi, R.P. / Hogle, J.M.
CitationJournal: J.Virol. / Year: 2009
Title: The crystal structure of PF-8, the DNA polymerase accessory subunit from Kaposi's sarcoma-associated herpesvirus.
Authors: Baltz, J.L. / Filman, D.J. / Ciustea, M. / Silverman, J.E. / Lautenschlager, C.L. / Coen, D.M. / Ricciardi, R.P. / Hogle, J.M.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: ORF59


Theoretical massNumber of molelcules
Total (without water)33,4151
Polymers33,4151
Non-polymers00
Water00
1
X: ORF59

X: ORF59


Theoretical massNumber of molelcules
Total (without water)66,8292
Polymers66,8292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_546x,x-y-1,-z+7/61
Buried area1570 Å2
ΔGint-7 kcal/mol
Surface area25700 Å2
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.300, 58.300, 386.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein ORF59


Mass: 33414.641 Da / Num. of mol.: 1 / Fragment: UNP residues 2-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q77ZG5
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 18% PEG 3350, 100 mM Tris HCl pH 8.2, 0.2 M lithium chloride, and 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 10612 / Num. obs: 10103 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 18.012
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 0.049 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.492 / % possible all: 62.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0093refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→29.15 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.917 / SU B: 36.824 / SU ML: 0.324 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.284 / ESU R Free: 0.391
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28131 465 4.8 %RANDOM
Rwork0.25169 ---
obs0.25311 9267 96.33 %-
all-10103 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.36 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å21.33 Å20 Å2
2--2.66 Å20 Å2
3----3.98 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 0 0 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.9522964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.65286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.99623.07778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.09315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.761513
X-RAY DIFFRACTIONr_chiral_restr0.1250.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0211587
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.76421415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4842282
X-RAY DIFFRACTIONr_scbond_it1.4424768
X-RAY DIFFRACTIONr_scangle_it2.5226682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.956 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.434 49 -
Rwork0.363 823 -
obs-823 86.85 %
Refinement TLS params.Method: refined / Origin x: 27.7329 Å / Origin y: -14.1581 Å / Origin z: 203.4016 Å
111213212223313233
T0.251 Å20.0206 Å20.0437 Å2-0.122 Å2-0.065 Å2--0.2145 Å2
L5.6048 °23.0278 °24.2485 °2-2.512 °22.9444 °2--5.6879 °2
S-0.1454 Å °0.3427 Å °0.2023 Å °-0.2688 Å °-0.077 Å °0.1615 Å °-0.2708 Å °0.1206 Å °0.2225 Å °

+
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