[English] 日本語
Yorodumi
- PDB-3wb0: HcgB from Methanocaldococcus jannaschii in complex with light-dec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wb0
TitleHcgB from Methanocaldococcus jannaschii in complex with light-decomposed FeGP cofactor of [Fe]-hydrogenase
ComponentsUncharacterized protein MJ0488
KeywordsTRANSFERASE / GTP-binding domain / Guanylyltransferase
Function / homology
Function and homology information


FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Helix hairpin bin / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FEG / Uncharacterized protein MJ0488
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis.
Authors: Fujishiro, T. / Tamura, H. / Schick, M. / Kahnt, J. / Xie, X. / Ermler, U. / Shima, S.
History
DepositionMay 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein MJ0488
B: Uncharacterized protein MJ0488
C: Uncharacterized protein MJ0488
D: Uncharacterized protein MJ0488
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6558
Polymers75,4854
Non-polymers2,1704
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-69 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.960, 119.340, 55.650
Angle α, β, γ (deg.)90.000, 115.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA2 - 1572 - 157
21SERSERBB2 - 1572 - 157
12LEULEUAA2 - 1592 - 159
22LEULEUCC2 - 1592 - 159
13LEULEUAA2 - 1592 - 159
23LEULEUDD2 - 1592 - 159
14SERSERBB2 - 1572 - 157
24SERSERCC2 - 1572 - 157
15SERSERBB2 - 1572 - 157
25SERSERDD2 - 1572 - 157
16LEULEUCC2 - 1592 - 159
26LEULEUDD2 - 1592 - 159

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Uncharacterized protein MJ0488


Mass: 18871.297 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 3-158
Source method: isolated from a genetically manipulated source
Details: NcoI-XhoI
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: HcgB, MJ0488 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q57912, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-FEG / 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine


Mass: 542.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23N6O11P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 %(w/v) PEG 8000, 0.1 M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationMonochromator: A double crystal Si(111) monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 46660 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.577 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-20.6620.3232.8813981696061050.41287.7
2-2.20.260.1855.672890810473102110.22597.5
2.2-2.40.180.1437.6419862724763160.1787.2
2.4-2.90.0670.09914.084463510558104410.11298.9
2.9-3.50.0480.07817.3824960595858690.08898.5
3.5-4.30.0430.07618.9414998363735360.08797.2
4.3-5.90.0420.07319.610884263725520.08496.8
5.9-80.0450.07718.3741039999700.08897.1
8-120.030.05721.0319904854660.06596.1
120.0310.06721.298672161940.07589.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRC

3brc


Resolution: 1.91→47.94 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2889 / WRfactor Rwork: 0.2347 / Occupancy max: 1 / Occupancy min: 0.55 / FOM work R set: 0.7972 / SU B: 8.608 / SU ML: 0.132 / SU R Cruickshank DPI: 0.225 / SU Rfree: 0.1928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 2329 5.1 %RANDOM
Rwork0.2266 ---
obs0.2291 45988 94.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.75 Å2 / Biso mean: 29.9177 Å2 / Biso min: 11.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.07 Å2
2--0.1 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.91→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 148 376 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195144
X-RAY DIFFRACTIONr_angle_refined_deg2.0312.0426905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39424.375192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.138151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0581544
X-RAY DIFFRACTIONr_chiral_restr0.1310.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023536
X-RAY DIFFRACTIONr_mcbond_it1.872.0662520
X-RAY DIFFRACTIONr_mcangle_it2.6523.0823143
X-RAY DIFFRACTIONr_scbond_it3.1772.5762624
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2050.07
12B2050.07
21A2020.08
22C2020.08
31A1970.09
32D1970.09
41B2000.06
42C2000.06
51B1990.09
52D1990.09
61C1950.09
62D1950.09
LS refinement shellResolution: 1.905→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.533 118 -
Rwork0.503 2342 -
all-2460 -
obs--68.47 %
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)
10.5204-0.11390.09690.80150.28240.14330.03910.0168-0.0144-0.1122-0.0393-0.0233-0.0241-0.00250.00030.05120.01790.01560.06810.00980.02416.3996-12.550413.8244
20.6479-0.24540.01930.8047-0.05490.0044-0.00350.0003-0.04070.09840.00530.099-0.00640.0038-0.00180.0368-0.00250.00440.05880.01590.03332.6309-13.979128.9427
30.04690.05690.02090.8041-0.07550.15890.02610.01390.0350.1791-0.0094-0.0222-0.0260.0142-0.01660.04690.00150.01170.0528-0.01480.05858.736212.029734.3669
40.62520.0527-0.06570.73240.05090.33910.10580.04070.0963-0.1563-0.03560.0891-0.0566-0.002-0.07030.0590.01860.00760.040.03260.065810.274414.173313.9859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION1A18 - 36
3X-RAY DIFFRACTION1A37 - 72
4X-RAY DIFFRACTION1A73 - 93
5X-RAY DIFFRACTION1A94 - 138
6X-RAY DIFFRACTION1A139 - 159
7X-RAY DIFFRACTION2B2 - 16
8X-RAY DIFFRACTION2B17 - 24
9X-RAY DIFFRACTION2B25 - 36
10X-RAY DIFFRACTION2B37 - 60
11X-RAY DIFFRACTION2B61 - 72
12X-RAY DIFFRACTION2B73 - 93
13X-RAY DIFFRACTION2B94 - 138
14X-RAY DIFFRACTION2B139 - 158
15X-RAY DIFFRACTION3C2 - 16
16X-RAY DIFFRACTION3C17 - 24
17X-RAY DIFFRACTION3C25 - 36
18X-RAY DIFFRACTION3C37 - 72
19X-RAY DIFFRACTION3C73 - 93
20X-RAY DIFFRACTION3C94 - 138
21X-RAY DIFFRACTION3C139 - 159
22X-RAY DIFFRACTION4D2 - 16
23X-RAY DIFFRACTION4D17 - 36
24X-RAY DIFFRACTION4D37 - 60
25X-RAY DIFFRACTION4D61 - 72
26X-RAY DIFFRACTION4D73 - 93
27X-RAY DIFFRACTION4D94 - 138
28X-RAY DIFFRACTION4D139 - 159

+
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