[English] 日本語
Yorodumi
- PDB-3wvb: HcgF from Methanocaldococcus jannaschii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wvb
TitleHcgF from Methanocaldococcus jannaschii
ComponentsUPF0254 protein MJ1251
KeywordsHYDROLASE / Thioesterase
Function / homologyFeGP cofactor biosynthesis protein HcgF / FeGP cofactor biosynthesis protein HcgF / UPF0254 protein MJ1251
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Nat Commun / Year: 2015
Title: Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor
Authors: Fujishiro, T. / Kahnt, J. / Ermler, U. / Shima, S.
History
DepositionMay 16, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0254 protein MJ1251
B: UPF0254 protein MJ1251


Theoretical massNumber of molelcules
Total (without water)38,5092
Polymers38,5092
Non-polymers00
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.310, 73.110, 45.530
Angle α, β, γ (deg.)90.000, 102.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 167 / Label seq-ID: 4 - 170

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein UPF0254 protein MJ1251


Mass: 19254.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1251 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q58649, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20%(w/v)PEG3000, 200mM sodium chloride, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.27 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2011
RadiationMonochromator: A Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 31585 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.62 % / Biso Wilson estimate: 21.029 Å2 / Rmerge(I) obs: 0.023 / Χ2: 1.024 / Net I/σ(I): 39.88
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.80.9960.04225.6216407501748550.0596.8
1.8-2.10.9980.03234.136652996398750.03799.1
2.1-2.30.9980.02738.6713933401939790.03299
2.3-2.50.9990.02445.7310979288428640.02899.3
2.5-2.80.9990.02345.6810688290028640.02798.8
2.8-3.30.9990.02148.089541279627500.02598.4
3.3-4.30.9990.01957.599018240923830.02298.9
4.3-5.90.9990.01956.124241124112210.02398.4
5.9-80.9980.02155.8518144734710.02599.6
8-120.9990.02458.128852312270.02898.3
120.9970.03154.08328101960.03695

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-labelled HcgF PDB ENTRY 3WVA

3wva


Resolution: 1.7→44.28 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.579 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 1600 5.1 %RANDOM
Rwork0.1452 ---
obs0.1476 31563 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.11 Å2 / Biso mean: 14.677 Å2 / Biso min: 5.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 0 333 3001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192726
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.9793666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.79824.958119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3531510
X-RAY DIFFRACTIONr_chiral_restr0.190.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021990
X-RAY DIFFRACTIONr_mcbond_it0.9260.8071340
X-RAY DIFFRACTIONr_mcangle_it1.3571.211673
X-RAY DIFFRACTIONr_scbond_it2.3631.1271386
Refine LS restraints NCS

Ens-ID: 1 / Number: 219 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 114 -
Rwork0.137 2196 -
all-2310 -
obs--96.49 %
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)
11.3234-0.1521-0.23290.5236-0.0731.0140.02540.11340.0393-0.0148-0.01490.0062-0.04520.0384-0.01050.0323-0.00240.00240.01350.00420.01634.7572-0.117311.2859
21.0673-0.18680.14830.43210.23330.3795-0.0161-0.052-0.00040.02310.00340.02430.0157-0.0050.01270.02020.00380.00340.0076-0.00090.002-7.9352-0.105821.5943
31.7967-0.3063-0.40660.8413-0.00450.69690.01330.11060.1262-0.0661-0.03950.0368-0.0631-0.03940.02620.0281-0.0007-0.00270.0128-0.00150.0269-15.8352-7.34493.2485
40.74250.0181-0.11450.27670.24670.4176-0.03360.0745-0.05220.00750.00620.01220.0073-0.01220.02740.0304-0.00760.01010.0084-0.00660.019-3.1307-17.75382.6714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION2A53 - 167
3X-RAY DIFFRACTION3B1 - 52
4X-RAY DIFFRACTION4B53 - 167

+
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