[English] 日本語
Yorodumi
- PDB-1jwb: Structure of the Covalent Acyl-Adenylate Form of the MoeB-MoaD Pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jwb
TitleStructure of the Covalent Acyl-Adenylate Form of the MoeB-MoaD Protein Complex
Components(MOLYBDOPTERIN ...) x 2
KeywordsLIGASE / MoeB: modified Rossmann fold / (2) Cys-X-X-Cys Zinc-binding motifs / MoaD: ubiquitin-like fold
Function / homology
Function and homology information


molybdopterin adenylyltransferase complex / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / molybdopterin synthase complex / ubiquitin-like modifier activating enzyme activity / sulfotransferase activity / thiosulfate-cyanide sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotidyltransferase activity / nucleotide binding ...molybdopterin adenylyltransferase complex / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / molybdopterin synthase complex / ubiquitin-like modifier activating enzyme activity / sulfotransferase activity / thiosulfate-cyanide sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotidyltransferase activity / nucleotide binding / protein homodimerization activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Molybdopterin synthase sulfurylase MoeB / Molybdopterin synthase sulfur carrier subunit / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Beta-grasp domain ...Molybdopterin synthase sulfurylase MoeB / Molybdopterin synthase sulfur carrier subunit / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Molybdopterin-synthase adenylyltransferase / Molybdopterin synthase sulfur carrier subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsLake, M.W. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H.
CitationJournal: Nature / Year: 2001
Title: Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex.
Authors: Lake, M.W. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionSep 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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
B: MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
D: MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0155
Polymers35,5072
Non-polymers5093
Water2,414134
1
B: MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
D: MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
hetero molecules

B: MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
D: MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,03110
Polymers71,0134
Non-polymers1,0176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area11780 Å2
ΔGint-108 kcal/mol
Surface area21350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.230, 77.230, 100.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe asymmetric unit contains a heterodimer comprised of (1) molecule of MoeB and (1) molecule of MoaD. The heterotetramer is generated by applying: -y+1,-x+1,1/2-z

-
Components

-
MOLYBDOPTERIN ... , 2 types, 2 molecules BD

#1: Protein MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN


Mass: 26741.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MoeB / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12282
#2: Protein MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1 / MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D


Mass: 8764.880 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MoaD / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30748

-
Non-polymers , 4 types, 137 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Lithium Sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlMoeB1drop
210 mg/mlMoaD1drop
31.7 M1reservoirLi2SO4
4100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18549 / Num. obs: 18549 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 1.3 / % possible all: 98.1
Reflection
*PLUS

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: REFMAC Dictionary
RfactorNum. reflection% reflectionSelection details
Rfree0.22494 773 4.3 %RANDOM
Rwork0.18792 ---
all0.1895 17376 --
obs0.1895 17376 98.9 %-
Displacement parametersBiso mean: 32.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 29 134 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.021
X-RAY DIFFRACTIONp_mcbond_it2.1011.5
X-RAY DIFFRACTIONp_mcangle_it3.4362
X-RAY DIFFRACTIONp_scbond_it4.9363
X-RAY DIFFRACTIONp_scangle_it7.54.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.3 % / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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