[English] 日本語
Yorodumi
- PDB-3d3r: Crystal structure of the hydrogenase assembly chaperone HypC/HupF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d3r
TitleCrystal structure of the hydrogenase assembly chaperone HypC/HupF family protein from Shewanella oneidensis MR-1
ComponentsHydrogenase assembly chaperone hypC/hupF
KeywordsCHAPERONE / small beta-barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


carbon dioxide binding / protein maturation / iron ion binding
Similarity search - Function
Hydrogenase expression/formation protein, HupF/HypC / HupF/HypC family / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
NiFe hydrogenase assembly chaperone HypC
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKim, Y. / Skarina, T. / Onopriyenko, O. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Hydrogenase Assembly Chaperone HypC/HupF Family Protein from Shewanella oneidensis MR-1.
Authors: Kim, Y. / Skarina, T. / Onopriyenko, O. / Edwards, A.M. / Savchenko, A. / Joachimiak, A.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydrogenase assembly chaperone hypC/hupF
B: Hydrogenase assembly chaperone hypC/hupF


Theoretical massNumber of molelcules
Total (without water)23,4632
Polymers23,4632
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-35.2 kcal/mol
Surface area11180 Å2
MethodPISA
2
A: Hydrogenase assembly chaperone hypC/hupF
B: Hydrogenase assembly chaperone hypC/hupF

A: Hydrogenase assembly chaperone hypC/hupF
B: Hydrogenase assembly chaperone hypC/hupF


Theoretical massNumber of molelcules
Total (without water)46,9264
Polymers46,9264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14100 Å2
ΔGint-144.5 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.864, 58.316, 51.924
Angle α, β, γ (deg.)90.00, 127.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-96-

HOH

-
Components

#1: Protein Hydrogenase assembly chaperone hypC/hupF


Mass: 11731.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-term 6-His-tag with TEV protease cleavage site / Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: hypC, SO_2092 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EF93
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M Ammonium citrate, 0.3M NDSB211, 0.5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2008 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.85→38.75 Å / Num. all: 15804 / Num. obs: 15804 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 30.17 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.92 / Num. unique all: 817 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→38.75 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.622 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.234 789 5 %RANDOM
Rwork0.202 ---
all0.203 14966 --
obs0.203 14966 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.876 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20.45 Å2
2---1.05 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 0 86 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221357
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9671846
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.52324.76965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48415248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7681510
X-RAY DIFFRACTIONr_chiral_restr0.1390.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021022
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2536
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2943
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6111.5869
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24821385
X-RAY DIFFRACTIONr_scbond_it3.6833536
X-RAY DIFFRACTIONr_scangle_it5.9624.5461
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 68 -
Rwork0.194 1121 -
obs-1189 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)
10.4576-0.1648-0.22810.33330.08370.1514-0.01390.0062-0.02660.00790.03530.01330.00650.02-0.0214-0.01890.0108-0.0101-0.0083-0.0056-0.049821.58559.990812.7794
20.9736-0.31790.17330.2548-0.09950.088-0.0113-0.0063-0.00930.00760.042-0.0039-0.0211-0.0051-0.0307-0.01330.0176-0.0026-0.01410.0089-0.048524.056117.965411.5437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-4 - 7617 - 97
2X-RAY DIFFRACTION2BB-3 - 7618 - 97

+
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