[English] 日本語
Yorodumi
- PDB-3c9b: Crystal structure of SeMet Vps75 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c9b
TitleCrystal structure of SeMet Vps75
ComponentsVacuolar protein sorting-associated protein 75
KeywordsCHAPERONE / chromatin / HAT / histone chaperone / Nucleus / Phosphoprotein / Protein transport / Transport
Function / homology
Function and homology information


H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding ...H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding / nucleus / cytosol
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 75
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.42 Å
AuthorsKeck, J.L. / Berndsen, C.E. / Tsubota, T. / Lindner, S.E. / Lee, S. / Holton, J.M. / Kaufman, P.D. / Denu, J.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75
Authors: Berndsen, C.E. / Tsubota, T. / Lindner, S.E. / Lee, S. / Holton, J.M. / Kaufman, P.D. / Keck, J.L. / Denu, J.M.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75


Theoretical massNumber of molelcules
Total (without water)60,4932
Polymers60,4932
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-23.2 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.203, 88.937, 94.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Vacuolar protein sorting-associated protein 75


Mass: 30246.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS75 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P53853
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M K Formate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2008 / Details: 0.9795,0.9686
RadiationMonochromator: KHOZU double flat crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.42→20 Å / Num. all: 26011 / Num. obs: 26011 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.5 % / Rmerge(I) obs: 0.217 / Net I/σ(I): 20.6
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 1.8 / % possible all: 100

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MAD / Resolution: 2.42→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.626 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1312 5 %RANDOM
Rwork0.212 ---
all0.214 26011 --
obs0.214 26009 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.141 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---1.18 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.42→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 279 3598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223409
X-RAY DIFFRACTIONr_angle_refined_deg0.9021.9484591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6625392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22624.104173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83515619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4131517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022592
X-RAY DIFFRACTIONr_nbd_refined0.2020.21493
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.26
X-RAY DIFFRACTIONr_mcbond_it0.7721.52034
X-RAY DIFFRACTIONr_mcangle_it1.32223198
X-RAY DIFFRACTIONr_scbond_it1.98431601
X-RAY DIFFRACTIONr_scangle_it3.1714.51393
LS refinement shellResolution: 2.42→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 89 -
Rwork0.287 1779 -
all-1868 -
obs--100 %
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)
11.1323-0.01070.5460.9951-0.19380.2990.02150.0139-0.02470.1269-0.0718-0.00870.0411-0.08120.0503-0.0466-0.01790.00560.0164-0.0156-0.051525.769470.580313.8667
20.13870.04530.2060.82760.29392.1444-0.02320.03590.0591-0.0955-0.181-0.1046-0.09350.04580.2042-0.02010.0185-0.0327-0.02780.0142-0.041734.386196.64544.8045
30.08060.15350.09150.55160.01640.19990.0361-0.0294-0.0092-0.0277-0.0592-0.0124-0.003-0.0250.023-0.03940.0095-0.00160.02580.0004-0.051230.255782.93111.1528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 221
2X-RAY DIFFRACTION2B17 - 221
3X-RAY DIFFRACTION3A260 - 384

+
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