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- PDB-1b9n: REGULATOR FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1b9n
TitleREGULATOR FROM ESCHERICHIA COLI
ComponentsPROTEIN (MODE)
KeywordsTRANSCRIPTION / DNA-BINDING / GENE REGULATION / WINGED HELIX TURN HELIX / MOLYBDATE / OB FOLD
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 / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
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 / 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 / : / Molybdenum-pterin binding domain / Mop domain profile. / Transport-associated OB, type 1 / TOBE domain / Molybdate/tungstate binding, C-terminal / Bacterial regulatory helix-turn-helix protein, lysR family / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / DNA-binding transcriptional dual regulator ModE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsHall, D.R. / Gourley, D.G. / Hunter, W.N.
Citation
Journal: EMBO J. / Year: 1999
Title: The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds.
Authors: Hall, D.R. / Gourley, D.G. / Leonard, G.A. / Duke, E.M. / Anderson, L.A. / Boxer, D.H. / Hunter, W.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Two crystal forms of ModE, the molybdate-dependent transcriptional regulator from Escherichia coli.
Authors: Hall, D.R. / Gourley, D.G. / Duke, E.M. / Leonard, G.A. / Anderson, L.A. / Pau, R.N. / Boxer, D.H. / Hunter, W.N.
#2: Journal: Eur.J.Biochem. / Year: 1997
Title: Characterisation of the molybdenum-responsive ModE regulatory protein and its binding to the promoter region of the modABCD (molybdenum transport) operon of Escherichia coli.
Authors: Anderson, L.A. / Palmer, T. / Price, N.C. / Bornemann, S. / Boxer, D.H. / Pau, R.N.
History
DepositionFeb 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MODE)
B: PROTEIN (MODE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2403
Polymers57,1812
Non-polymers591
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-50 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.110, 127.360, 62.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (MODE)


Mass: 28590.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9G8
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 59 %
Description: A STARTING MODEL WAS DERIVED FROM MAD PHASED MAPS OF A SELENOMETHIONYL DERIVATIVE OF THIS PROTEIN.
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 277 K / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mM1dropNa2WO4
210-18 %PEG80001reservoir
350 mMcacodylic acid1reservoir
4100 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→28.63 Å / Num. obs: 268449 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 31.98 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.4
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 4 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 37763 / Num. measured all: 268449
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.09→28.63 Å / SU B: 5.01249 / SU ML: 0.13767 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.20739 / ESU R Free: 0.20519
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1934 5 %RANDOM
Rwork0.214 ---
obs-37763 99 %-
Displacement parametersBiso mean: 39.12 Å2
Refinement stepCycle: LAST / Resolution: 2.09→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 1 309 4132
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.1712
X-RAY DIFFRACTIONp_mcangle_it4.2613
X-RAY DIFFRACTIONp_scbond_it3.6712
X-RAY DIFFRACTIONp_scangle_it5.0313
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.2370.15
X-RAY DIFFRACTIONp_singtor_nbd0.2030.3
X-RAY DIFFRACTIONp_multtor_nbd0.2650.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.210.3
X-RAY DIFFRACTIONp_planar_tor5.57
X-RAY DIFFRACTIONp_staggered_tor19.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.120
X-RAY DIFFRACTIONp_special_tor

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