[English] 日本語
Yorodumi
- PDB-5o4h: HcgC from Methanococcus maripaludis cocrystallized with SAM and p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o4h
TitleHcgC from Methanococcus maripaludis cocrystallized with SAM and pyridinol
ComponentsHcgC
KeywordsTRANSFERASE / methyltransferases / biosynthesis / protein structures / enzyme catalysis / mutagenesis / [Fe]-hydrogenase / pyridinol / Hmd
Function / homologyFeGP cofactor biosynthesis protein, methyltransferase HcgC / FeGP cofactor biosynthesis protein, methyltransferase HcgC / ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein
Function and homology information
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWagner, T. / Bai, L. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC.
Authors: Bai, L. / Wagner, T. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.
History
DepositionMay 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HcgC
B: HcgC
C: HcgC
D: HcgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,52423
Polymers123,7704
Non-polymers3,75419
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-123 kcal/mol
Surface area41240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.168, 77.736, 100.991
Angle α, β, γ (deg.)90.00, 110.87, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
HcgC


Mass: 30942.623 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A his-tagged has been placed in the C-terminal of the construct
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Cell line: / / Gene: MMP1498 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q6LX54

-
Non-polymers , 6 types, 718 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.17 Å3/Da / Density % sol: 43.4 % / Description: Thick transparent hexagonal brick
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 5 mg/ml of pure HcgC containing 2 mM SAM and 2 mM pyridinol was used and mixed at a ratio of 1 ul with 1 ul of precipitant composed of 50% v/v PEG 400, 100 mM NaAcetate pH 4.5 and 200 mM LiSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.75→47.85 Å / Num. obs: 106203 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.041 / Net I/σ(I): 9.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 15490 / CC1/2: 0.421 / Rpim(I) all: 0.331 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D4V

5d4v


Resolution: 1.75→47.85 Å / Cor.coef. Fo:Fc: 0.9603 / Cor.coef. Fo:Fc free: 0.9512 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 5307 5 %RANDOM
Rwork0.1675 ---
obs0.1688 106177 99.6 %-
Displacement parametersBiso mean: 37.97 Å2
Baniso -1Baniso -2Baniso -3
1--3.4782 Å20 Å20.8315 Å2
2--0.5191 Å20 Å2
3---2.9591 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: 1 / Resolution: 1.75→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16869 0 200 699 17768
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117269HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2131430HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4045SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes223HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2365HARMONIC20
X-RAY DIFFRACTIONt_it17269HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.47
X-RAY DIFFRACTIONt_other_torsion13.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1177SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19229SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2638 409 5.25 %
Rwork0.2254 7388 -
all0.2274 7797 -
obs--99.6 %
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)
10.71280.06360.27151.10950.19711.11570.00560.090.0192-0.16730.03020.0052-0.03330.0332-0.0358-0.037-0.03160.0196-0.04450.0295-0.058832.54782.6335-13.8605
20.55820.14960.22660.9658-0.03871.5873-0.0226-0.02-0.06050.1875-0.032-0.2034-0.16050.12320.0547-0.0501-0.0318-0.0358-0.03190.0279-0.027142.563110.428723.2604
30.68950.15740.97441.05820.45181.6311-0.0617-0.08940.0838-0.0718-0.070.324-0.0448-0.16930.1317-0.1121-0.0009-0.027-0.0813-0.01320.0786-0.0026-2.4137-1.628
40.6401-0.33040.33370.4673-0.06462.1783-0.043-0.1173-0.09480.1904-0.02440.11490.2457-0.16850.06740.0085-0.01840.0808-0.08-0.0045-0.029916.4145-11.247632.2562
50.1535-0.0923-0.10650.25370.4058-0.0594-0.00060.0006-0.0021-0.0023-0.00160.00290.00250.0020.00220.0024-0.0014-0.00170.0015-0.0052-0.004433.86979.7545.2139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ H|* }

+
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