[English] 日本語
Yorodumi
- PDB-2op6: Peptide-binding domain of Heat shock 70 kDa protein D precursor f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2op6
TitlePeptide-binding domain of Heat shock 70 kDa protein D precursor from C.elegans
ComponentsHeat shock 70 kDa protein D
KeywordsPEPTIDE BINDING PROTEIN / hsp70/peptide-binding domain / structural genomics / APC90014.13 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / endoplasmic reticulum chaperone complex / misfolded protein binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / rough endoplasmic reticulum / cellular response to unfolded protein / : / endoplasmic reticulum unfolded protein response ...RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / endoplasmic reticulum chaperone complex / misfolded protein binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / rough endoplasmic reticulum / cellular response to unfolded protein / : / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / unfolded protein binding / protein refolding / endoplasmic reticulum lumen / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Endoplasmic reticulum targeting sequence. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family ...Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Endoplasmic reticulum targeting sequence. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endoplasmic reticulum chaperone BiP homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOsipiuk, J. / Duggan, E. / Gu, M. / Voisine, C. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray structure of peptide-binding domain of Heat shock 70 kDa protein D precursor from C.elegans
Authors: Osipiuk, J. / Duggan, E. / Gu, M. / Voisine, C. / Morimoto, R.I. / Joachimiak, A.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock 70 kDa protein D


Theoretical massNumber of molelcules
Total (without water)16,5461
Polymers16,5461
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.172, 26.688, 60.995
Angle α, β, γ (deg.)90.00, 115.14, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Heat shock 70 kDa protein D


Mass: 16546.467 Da / Num. of mol.: 1 / Fragment: hsp70 peptide-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: hsp-4, hsp70d / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20163
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M Tri-sodium citrate, 0.1 M HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9797 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 12, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.85→30.44 Å / Num. all: 12530 / Num. obs: 12530 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.97 / Num. unique all: 754 / % possible all: 55.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YUW

1yuw


Resolution: 1.85→30.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.963 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1237 9.9 %RANDOM
Rwork0.1689 ---
all0.1735 11283 --
obs0.1735 11283 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.29 Å2
2---0.85 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 0 166 1311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221251
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9721715
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02926.12962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50415237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9158
X-RAY DIFFRACTIONr_chiral_restr0.10.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02966
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2531
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2857
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8951.5811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33521303
X-RAY DIFFRACTIONr_scbond_it2.3223474
X-RAY DIFFRACTIONr_scangle_it3.7454.5398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 47 -
Rwork0.248 460 -
obs-507 49.56 %
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)
12.4533-0.3127-1.09945.5953-0.22530.51670.0358-0.09360.026-0.2090.06210.56810.10580.0692-0.09790.00960.0021-0.0391-0.0638-0.00790.0572-13.4046.84368.6404
20.36850.04010.22822.9671-1.2030.71020.0726-0.14280.01740.0489-0.03840.1771-0.02160.0396-0.03420.0101-0.00370.0026-0.02360.00250.0017-8.70854.066915.3679
30.2448-0.02280.28210.175-0.13140.5689-0.01430.0029-0.01960.0226-0.00230.0228-0.00670.05130.01660.00660.0063-0.0062-0.010.0057-0.0016-0.2501-0.878316.4309
42.71941.24293.97980.83961.99395.9372-0.14830.0550.1222-0.0048-0.02190.0049-0.21890.07270.1702-0.00530.006-0.00460.0101-0.0001-0.02024.38351.77168.9508
514.1613-1.0768-1.46821.2421-1.34144.2376-0.0907-0.22760.0087-0.3157-0.02350.23440.02470.01570.1142-0.04730.0124-0.0406-0.0613-0.01370.0227-19.4827-2.5625.173
617.7251-3.732818.22373.1433-2.256219.79750.9544-2.10960.2520.4326-0.69350.29990.8313-1.0241-0.2609-0.0906-0.20440.1480.3671-0.07810.0075-19.866-5.10523.6095
76.5371-5.7751-4.567121.48537.677113.8749-0.0952-0.2608-0.34050.72490.17880.57960.5706-0.5575-0.08360.0127-0.0317-0.01740.01410.05070.0378-1.7142-4.196625.543
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA419 - 4273 - 11
2X-RAY DIFFRACTION2AA428 - 44812 - 32
3X-RAY DIFFRACTION3AA449 - 51533 - 99
4X-RAY DIFFRACTION4AA516 - 533100 - 117
5X-RAY DIFFRACTION5AA534 - 547118 - 131
6X-RAY DIFFRACTION6AA548 - 562132 - 146
7X-RAY DIFFRACTION7AA563 - 568147 - 152

+
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