[English] 日本語
Yorodumi
- PDB-1ejf: CRYSTAL STRUCTURE OF THE HUMAN CO-CHAPERONE P23 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ejf
TitleCRYSTAL STRUCTURE OF THE HUMAN CO-CHAPERONE P23
ComponentsProstaglandin E synthase 3
KeywordsCHAPERONE / Co-Chaperone / Beta-Sandwich
Function / homology
Function and homology information


prostaglandin-E synthase / prostaglandin-E synthase activity / telomerase activity / prostanoid biosynthetic process / Aryl hydrocarbon receptor signalling / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / telomerase holoenzyme complex / prostaglandin biosynthetic process / protein folding chaperone complex / telomerase holoenzyme complex assembly ...prostaglandin-E synthase / prostaglandin-E synthase activity / telomerase activity / prostanoid biosynthetic process / Aryl hydrocarbon receptor signalling / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / telomerase holoenzyme complex / prostaglandin biosynthetic process / protein folding chaperone complex / telomerase holoenzyme complex assembly / : / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / DNA polymerase binding / positive regulation of telomere maintenance via telomerase / telomere maintenance / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Hsp90 protein binding / unfolded protein binding / protein folding / protein-folding chaperone binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / chromosome, telomeric region / protein stabilization / signal transduction / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Prostaglandin E synthase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsWeaver, A.J. / Sullivan, W.P. / Felts, S.J. / Owen, B.A.L. / Toft, D.O.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure and activity of human p23, a heat shock protein 90 co-chaperone.
Authors: Weaver, A.J. / Sullivan, W.P. / Felts, S.J. / Owen, B.A. / Toft, D.O.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
Revision 1.4Oct 28, 2020Group: Derived calculations / Structure summary / Category: entity / entity_name_com / struct_site
Item: _entity.pdbx_description / _struct_site.pdbx_auth_asym_id ..._entity.pdbx_description / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prostaglandin E synthase 3
B: Prostaglandin E synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0735
Polymers29,7852
Non-polymers2883
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-24 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.802, 61.802, 162.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Prostaglandin E synthase 3 / p23 / Hsp90 co-chaperone


Mass: 14892.471 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: DE3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q15185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, bicine, tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.9-2.1 Mammonium sulfate1reservoir
20.1 MBicine1reservoirpH9.0
320 mg/mlprotein1drop
410 mMTris-HCl1droppH7.5

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9159
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.49→100 Å / Num. all: 11727 / Num. obs: 11651 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.7
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.074 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 11743 / Num. measured all: 97860 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 98.8 % / Num. unique obs: 1651 / Num. measured obs: 11297 / Mean I/σ(I) obs: 8.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.49→100 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 554 4.8 %RANDOM
Rwork0.236 ---
all0.238 11727 --
obs0.238 11651 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.8 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--2.55 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.49→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 15 58 1913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.002
X-RAY DIFFRACTIONc_angle_deg0.6
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d0.39
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_scangle_it4.892.5
LS refinement shellResolution: 2.49→2.65 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 94 5 %
Rwork0.3 1800 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.39
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scangle_it4.892.5
LS refinement shell
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.3

+
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