[English] 日本語
Yorodumi
- PDB-1h9s: Molybdate bound complex of Dimop domain of ModE from E.coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h9s
TitleMolybdate bound complex of Dimop domain of ModE from E.coli
Components(MOLYBDENUM TRANSPORT PROTEIN MODE) x 2
KeywordsTRANSCRIPTION REGULATOR
Function / homology
Function and homology information


ModE complex / molybdate ion transport / negative regulation of DNA-templated transcription initiation / molybdenum ion binding / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / cytosol / cytoplasm
Similarity search - Function
Molybdenum-binding protein ModE, N-terminal / Molybdate-dependent transcriptional regulator ModE / Mop domain profile. / Molybdenum-pterin binding domain / Transport-associated OB, type 1 / TOBE domain / Molybdate/tungstate binding, C-terminal / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain ...Molybdenum-binding protein ModE, N-terminal / Molybdate-dependent transcriptional regulator ModE / Mop domain profile. / Molybdenum-pterin binding domain / Transport-associated OB, type 1 / TOBE domain / Molybdate/tungstate binding, C-terminal / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MOLYBDATE ION / DNA-binding transcriptional dual regulator ModE / Transcriptional regulator ModE
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsGourley, D.G. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Oxyanion Binding Alters Conformational and Quaternary Structure of the C-Terminal Domain of the Transcriptional Regulator Mode; Implications for Molybdate-Dependant Regulation, Signalling, Storage and Transport
Authors: Gourley, D.G. / Schuttelkopf, A.W. / Anderson, L.A. / Price, N.C. / Boxer, D.H. / Hunter, W.N.
History
DepositionMar 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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: MOLYBDENUM TRANSPORT PROTEIN MODE
B: MOLYBDENUM TRANSPORT PROTEIN MODE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4194
Polymers30,0992
Non-polymers3202
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.340, 73.340, 49.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.125, -0.974, 0.187), (-0.973, -0.157, -0.171), (0.196, -0.16, -0.967)
Vector: 27.88846, 42.33894, 51.43727)

-
Components

#1: Protein MOLYBDENUM TRANSPORT PROTEIN MODE


Mass: 15048.901 Da / Num. of mol.: 1 / Fragment: MOLYBDATE BINDING DOMAIN RESIDUES 123-260 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P46930, UniProt: P0A9G8*PLUS
#2: Protein MOLYBDENUM TRANSPORT PROTEIN MODE


Mass: 15049.888 Da / Num. of mol.: 1 / Fragment: MOLYBDATE BINDING DOMAIN RESIDUES 123-260 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P46930, UniProt: P0A9G8*PLUS
#3: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: MoO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION FROM LEU 123 MET BINDS MOLYBDENUM. REGULATES MOD OPERON BY BINDING ...CHAIN A, B ENGINEERED MUTATION FROM LEU 123 MET BINDS MOLYBDENUM. REGULATES MOD OPERON BY BINDING TO THE MODABCD PROMOTER REGION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growpH: 7.6 / Details: pH 7.60
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
116 mg/mlprotein1drop
250 mMTris-HCl1drop
310 mM1dropNa2MoO4
41.0 Mtrisodium citrate1reservoir
5100 mMHEPES1reservoir
610 %ethylene glycol1reservoiror 1.4M ammonium sulfate
7100 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 20410 / % possible obs: 97.9 % / Redundancy: 9 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.49 / Net I/σ(I): 27.8
Reflection
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 30 Å / Num. obs: 22803 / % possible obs: 98.1 % / Num. measured all: 272924 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 84.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.9

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B9N

1b9n


Resolution: 1.82→20 Å / SU B: 2.95 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1182 5 %RANDOM
Rwork0.188 ---
obs-22803 98.1 %-
Displacement parametersBiso mean: 34.2 Å2
Refinement stepCycle: LAST / Resolution: 1.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 10 227 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.722
X-RAY DIFFRACTIONp_mcangle_it2.2663
X-RAY DIFFRACTIONp_scbond_it1.7772
X-RAY DIFFRACTIONp_scangle_it2.8253
X-RAY DIFFRACTIONp_plane_restr0.0290.03
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.2190.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2550.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1330.3
X-RAY DIFFRACTIONp_planar_tor3.1097
X-RAY DIFFRACTIONp_staggered_tor14.02115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.0920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
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