[English] 日本語
Yorodumi
- PDB-1h9m: Two crystal structures of the cytoplasmic molybdate-binding prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h9m
TitleTwo crystal structures of the cytoplasmic molybdate-binding protein ModG suggest a novel cooperative binding mechanism and provide insights into ligand-binding specificity. PEG-grown form with molybdate bound
ComponentsMOLYBDENUM-BINDING-PROTEIN
KeywordsBINDING PROTEIN / MOLYBDATE HOMEOSTASIS
Function / homology
Function and homology information


molybdate ion transport
Similarity search - Function
: / Molybdenum-pterin binding domain / Mop domain profile. / Transport-associated OB, type 1 / TOBE domain / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MOLYBDATE ION / Potential molybdenum-pterin-binding-protein
Similarity search - Component
Biological speciesAZOTOBACTER VINELANDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDelarbre, L. / Stevenson, C.E.M. / White, D.J. / Mitchenall, L.A. / Pau, R.N. / Lawson, D.M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Two Crystal Structures of the Cytoplasmic Molybdate-Binding Protein Modg Suggest a Novel Cooperative Binding Mechanism and Provide Insights Into Ligand-Binding Specificity
Authors: Delarbre, L. / Stevenson, C.E.M. / White, D.J. / Mitchenall, L.A. / Pau, R.N. / Lawson, D.M.
History
DepositionMar 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MOLYBDENUM-BINDING-PROTEIN
B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,58910
Polymers29,3102
Non-polymers1,2808
Water1,42379
1
A: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

A: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

A: MOLYBDENUM-BINDING-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,88415
Polymers43,9653
Non-polymers1,91912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
2
B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules

B: MOLYBDENUM-BINDING-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,88415
Polymers43,9653
Non-polymers1,91912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.960, 81.960, 93.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1142-

MOO

21A-1142-

MOO

31A-1143-

MOO

41A-1143-

MOO

51B-1142-

MOO

61B-1142-

MOO

71B-1143-

MOO

81B-1143-

MOO

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.50232, 0.86468, -0.00062), (0.86468, 0.50232, 0.00259), (0.00255, 0.00076, -1)
Vector: 0.11845, -0.19583, 93.3504)
DetailsBIOMOLECULE

-
Components

#1: Protein MOLYBDENUM-BINDING-PROTEIN / MODG


Mass: 14654.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Strain: E162 / Cellular location: CYTOPLASM / Gene: MODG / Gene (production host): MODG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q44529
#2: Chemical
ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: MoO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.34 Å3/Da / Density % sol: 41 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: VAPOUR DIFFUSION. 20% PEG 4000, 5% ISOPROPANOL IN 100MM HEPES PH7.5 WITH 2MM NA2MOO4., pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %(w/v)PEG40001reservoir
25 %(v/v)isopropanol1reservoir
3100 mMHEPES1reservoirpH7.5
42 mM1reservoirNa2MoO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→41 Å / Num. obs: 28231 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 41.7
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 8.8 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H9J

1h9j


Resolution: 1.65→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1385 5 %RANDOM
Rwork0.191 ---
obs-28231 98.7 %-
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 32 79 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.433
X-RAY DIFFRACTIONp_mcangle_it3.9675
X-RAY DIFFRACTIONp_scbond_it4.9956
X-RAY DIFFRACTIONp_scangle_it6.9188
X-RAY DIFFRACTIONp_plane_restr0.02330.03
X-RAY DIFFRACTIONp_chiral_restr0.1620.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2650.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1310.3
X-RAY DIFFRACTIONp_planar_tor4.47
X-RAY DIFFRACTIONp_staggered_tor14.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor51.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
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