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- PDB-1h9s: Molybdate bound complex of Dimop domain of ModE from E.coli -

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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 / negative regulation of DNA-templated transcription initiation / molybdate ion transport / molybdenum ion binding / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding ...ModE complex / negative regulation of DNA-templated transcription initiation / molybdate ion transport / molybdenum ion binding / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / 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 / : / Molybdenum-pterin binding domain / Mop domain profile. / Transport-associated OB, type 1 / TOBE domain / Molybdate/tungstate binding, C-terminal / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family ...Molybdenum-binding protein ModE, N-terminal / Molybdate-dependent transcriptional regulator ModE / : / Molybdenum-pterin binding domain / Mop domain profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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


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

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Experimental details

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Experiment

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

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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

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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

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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

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