[English] 日本語
Yorodumi
- PDB-3i2v: Crystal structure of human MOCS3 rhodanese-like domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i2v
TitleCrystal structure of human MOCS3 rhodanese-like domain
ComponentsAdenylyltransferase and sulfurtransferase MOCS3
KeywordsTRANSFERASE / RHODANESE / SULFURTRANSFERASE / MOCS3 / UBA4 / Structural Genomics / Ubiquitin biology / Structural Genomics Consortium / SGC / ATP-binding / Cytoplasm / Molybdenum cofactor biosynthesis / Multifunctional enzyme / Nucleotide-binding / tRNA processing
Function / homology
Function and homology information


URM1 activating enzyme activity / : / molybdopterin synthase sulfurtransferase / molybdopterin-synthase sulfurtransferase activity / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / tRNA thio-modification / Molybdenum cofactor biosynthesis / tRNA wobble position uridine thiolation / protein urmylation ...URM1 activating enzyme activity / : / molybdopterin synthase sulfurtransferase / molybdopterin-synthase sulfurtransferase activity / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / tRNA thio-modification / Molybdenum cofactor biosynthesis / tRNA wobble position uridine thiolation / protein urmylation / protein modification by small protein conjugation / molybdopterin cofactor biosynthetic process / sulfurtransferase activity / thiosulfate sulfurtransferase activity / tRNA wobble uridine modification / Mo-molybdopterin cofactor biosynthetic process / nucleotidyltransferase activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Adenylyltransferase and sulfurtransferase MOCS3/Uba4 / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Adenylyltransferase and sulfurtransferase MOCS3/Uba4 / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Adenylyltransferase and sulfurtransferase MOCS3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsBacik, J.P. / Walker, J.R. / Lopez, L. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the human MOCS3 rhodanese-like domain
Authors: Bacik, J.P. / Walker, J.R. / Lopez, L. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylyltransferase and sulfurtransferase MOCS3


Theoretical massNumber of molelcules
Total (without water)14,2221
Polymers14,2221
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.817, 31.911, 50.640
Angle α, β, γ (deg.)90.00, 110.16, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Adenylyltransferase and sulfurtransferase MOCS3 / Molybdenum cofactor synthesis protein 3 / Molybdopterin synthase sulfurylase / MPT synthase ...Molybdenum cofactor synthesis protein 3 / Molybdopterin synthase sulfurylase / MPT synthase sulfurylase / Adenylyltransferase MOCS3 / Sulfurtransferase MOCS3


Mass: 14222.272 Da / Num. of mol.: 1 / Fragment: RHODANESE-LIKE DOMAIN, residues 335-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOCS3, MOCS3_HUMAN, UBA4 / Plasmid: pET28aLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O95396, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.96 Å3/Da / Density % sol: 37.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 21% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.072 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.25→24.26 Å / Num. obs: 30819 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 12.61 Å2 / Rsym value: 0.063 / Net I/σ(I): 33.7
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 5 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.83 / % possible all: 66.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.25→24.258 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 20.78 / Stereochemistry target values: ML
Details: INITIAL DATASET USED TO LOCATE SEMET COLLECTED AT 0.96426 A
RfactorNum. reflection% reflection
Rfree0.2043 1457 4.98 %
Rwork0.159 --
obs0.1614 29228 94.89 %
all-1019 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.255 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 12.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.354 Å2-0 Å20.33 Å2
2---0.384 Å2-0 Å2
3---0.738 Å2
Refinement stepCycle: LAST / Resolution: 1.25→24.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 0 190 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151004
X-RAY DIFFRACTIONf_angle_d1.5931369
X-RAY DIFFRACTIONf_dihedral_angle_d15.521375
X-RAY DIFFRACTIONf_chiral_restr0.108162
X-RAY DIFFRACTIONf_plane_restr0.01175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.29470.33581010.27612039X-RAY DIFFRACTION71
1.2947-1.34650.22821300.17772704X-RAY DIFFRACTION93
1.3465-1.40780.20281570.1312834X-RAY DIFFRACTION97
1.4078-1.4820.20381350.13252826X-RAY DIFFRACTION97
1.482-1.57480.20941290.12522895X-RAY DIFFRACTION98
1.5748-1.69640.17541540.13042831X-RAY DIFFRACTION98
1.6964-1.86710.19941640.14182906X-RAY DIFFRACTION99
1.8671-2.13710.18431560.14522904X-RAY DIFFRACTION99
2.1371-2.69190.21081680.15352919X-RAY DIFFRACTION100
2.6919-24.26240.19771630.17122913X-RAY DIFFRACTION97

+
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