[English] 日本語
Yorodumi
- PDB-8hlg: Crystal structure of MoaE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hlg
TitleCrystal structure of MoaE
ComponentsMolybdenum cofactor biosynthesis protein D/E
KeywordsTRANSFERASE / cofactor / biosynthesis
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain superfamily
Similarity search - Domain/homology
Molybdenum cofactor biosynthesis protein D/E
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCai, J. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0503900 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: MoaE Is Involved in Response to Oxidative Stress in Deinococcus radiodurans.
Authors: Cai, J. / Zhang, M. / Chen, Z. / Zhao, Y. / Xu, H. / Tian, B. / Wang, L. / Hua, Y.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein D/E
B: Molybdenum cofactor biosynthesis protein D/E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4114
Polymers38,2192
Non-polymers1922
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-47 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.020, 94.950, 101.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-334-

HOH

-
Components

#1: Protein Molybdenum cofactor biosynthesis protein D/E


Mass: 19109.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Gene: DR_2607 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RR88
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Lithium Sulfate, Tris-HCl, PEG 3350

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 20539 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Net I/σ(I): 16.56
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.050.5614770.9090.6081
2.05-2.110.44314780.930.4791
2.11-2.170.38314130.940.4151
2.17-2.240.2913750.9670.3151
2.24-2.310.26113400.9690.2851
2.31-2.390.21113040.980.2291
2.39-2.480.16912460.9860.1831
2.48-2.580.13512230.990.1461
2.58-2.70.10711690.9940.1171
2.7-2.830.09211070.9950.11
2.83-2.980.06910620.9970.0751
2.98-3.160.06110060.9970.0661
3.16-3.380.0559400.9970.0611
3.38-3.650.0468810.9980.0511
3.65-40.0478280.9980.0511
4-4.470.0437420.9980.0461
4.47-5.160.046680.9980.0441
5.16-6.320.045710.9980.0431
6.32-8.940.0364450.9990.0391
8.94-300.0282640.9990.0311

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
BALBESphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.65 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 1011 4.93 %
Rwork0.1944 --
obs0.1965 20510 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 10 77 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052185
X-RAY DIFFRACTIONf_angle_d0.7222973
X-RAY DIFFRACTIONf_dihedral_angle_d16.73783
X-RAY DIFFRACTIONf_chiral_restr0.054321
X-RAY DIFFRACTIONf_plane_restr0.009387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.28161440.25452745X-RAY DIFFRACTION100
2.11-2.240.26171240.22692748X-RAY DIFFRACTION100
2.24-2.410.25921420.22222751X-RAY DIFFRACTION100
2.41-2.650.27541330.22252783X-RAY DIFFRACTION100
2.65-3.040.27161670.23212752X-RAY DIFFRACTION100
3.04-3.820.2371500.19952810X-RAY DIFFRACTION100
3.82-29.650.19931510.15882910X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.5328 Å / Origin y: 63.1665 Å / Origin z: 35.8742 Å
111213212223313233
T0.3106 Å2-0.0446 Å20.005 Å2-0.3391 Å2-0.0396 Å2--0.2976 Å2
L1.0401 °2-0.087 °2-0.0577 °2-0.9056 °2-0.2817 °2--1.359 °2
S0.0884 Å °-0.0948 Å °0.0122 Å °-0.0518 Å °-0.0163 Å °0.0491 Å °-0.0799 Å °0.2674 Å °0 Å °
Refinement TLS groupSelection details: all

+
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