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- PDB-1o7l: Molybdate-activated form of ModE from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1o7l
TitleMolybdate-activated form of ModE from Escherichia coli
ComponentsTRANSCRIPTIONAL REGULATOR MODE
KeywordsTRANSCRIPTION REGULATION / DNA BINDING / MOLYBDATE / MOP / WINGED HELIX-TURN-HELIX / TRANSCRIPTIONAL REGULATOR / ACTIVATOR
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 / cytoplasm / 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 / 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 / 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
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: 2.75 Å
AuthorsSchuttelkopf, A.W. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of Activated Mode Reveals Conformational Changes Involving Both Oxyanion and DNA-Binding Domains
Authors: Schuttelkopf, A.W. / Boxer, D.H. / Hunter, W.N.
History
DepositionNov 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR MODE
B: TRANSCRIPTIONAL REGULATOR MODE
C: TRANSCRIPTIONAL REGULATOR MODE
D: TRANSCRIPTIONAL REGULATOR MODE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,10811
Polymers113,2334
Non-polymers8757
Water48627
1
A: TRANSCRIPTIONAL REGULATOR MODE
B: TRANSCRIPTIONAL REGULATOR MODE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9725
Polymers56,6162
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: TRANSCRIPTIONAL REGULATOR MODE
D: TRANSCRIPTIONAL REGULATOR MODE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1366
Polymers56,6162
Non-polymers5204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.831, 78.831, 195.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999143, 0.005943, -0.040958), (-0.005649, -0.999957, -0.007293), (-0.041, -0.007055, 0.999134)56.754, 61.667, 1.017
2given(-0.999359, -0.004053, -0.035567), (0.004768, -0.999788, -0.020032), (-0.035478, -0.020189, 0.999166)56.744, 61.655, 1.486
DetailsBIOMOLECULE 1:BIOMOLECULE 2:

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Components

#1: Protein
TRANSCRIPTIONAL REGULATOR MODE / MODE / MODR


Mass: 28308.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PLAA6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46930, UniProt: P0A9G8*PLUS
#2: Chemical
ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: MoO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMODE-MO COMPLEX ACTS AS A REPRESSOR OF THE MODABCD OPERON THAT IS INVOLVED IN THE TRANSPORT OF ...MODE-MO COMPLEX ACTS AS A REPRESSOR OF THE MODABCD OPERON THAT IS INVOLVED IN THE TRANSPORT OF MOLYBDATE. BINDING OF MOLYBDENUM CAUSES CHANGE IN THE CONFORMATION OF MODE, WHICH IN TURN INCREASES MODE AFFINITY TO A DNA REGION UPSTREAM OF THE MODABCD OPERON. MODE IS ALSO AN ENHANCER OF GENES CODING FOR MOLYBDOENZYMES.

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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: 2.68 Å3/Da / Density % sol: 54 %
Description: THE DATA IS PARTIALLY MEROHEDRALLY TWINNED WITH A TWIN FRACTION OF APPROXIMATELY 0.33 AND A TWIN LAW OF H, -K, -L.
Crystal growpH: 7.5
Details: 27% PEG1000, 70MM CACL2, 1.5% 1,2,3-HEPTANETRIOL, 70MM HEPES PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
170 mMsodium HEPES1reservoirpH7.5
227 %(w/v)PEG10001reservoir
370 mM1reservoirCaCl2
41.5 %heptanetriol1drop
52.2 mM1dropNa2MoO4
63.9 mg/mlprotein1drop
70.140 mMDNA oligonucleotide1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 15, 1999 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 29920 / % possible obs: 96 % / Redundancy: 4.6 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.1
Reflection shellResolution: 2.75→2.81 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.8 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 2992 / Num. measured all: 124769
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H9R

1h9r


Resolution: 2.75→25 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TWIN_LSQ
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1005 3.4 %THIN RESOLUTION SHELLS
Rwork0.207 ---
obs0.207 29319 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1093 Å2 / ksol: 0.264797 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.2 Å20 Å20 Å2
2---7.2 Å20 Å2
3---14.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7798 0 27 27 7852
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.7
X-RAY DIFFRACTIONc_mcangle_it2.262.3
X-RAY DIFFRACTIONc_scbond_it1.872.3
X-RAY DIFFRACTIONc_scangle_it2.922.9
Refine LS restraints NCSRms dev position: 1.38 Å / Weight position: 0
LS refinement shellResolution: 2.75→2.85 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 134 4.5 %
Rwork0.319 2961 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MOO4.PARAMMOO4.TOP
Refinement
*PLUS
Rfactor Rfree: 0.255 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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