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- PDB-1mjm: METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CO... -

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Basic information

Entry
Database: PDB / ID: 1mjm
TitleMETHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE
Components
  • HALF CONSENSUS DNA OPERATOR DUPLEX
  • METHIONINE REPRESSOR
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / METJ / METHIONINE REPRESSOR / SHEET-HELIX-HELIX / S-ADENOSYL METHIONINE / DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


methionine biosynthetic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
MET Apo-Repressor, subunit A / MET Apo-Repressor, subunit A / Methionine repressor MetJ / Methionine repressor MetJ domain superfamily / Met Apo-repressor, MetJ / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGarvie, C.W. / Phillips, S.E.V.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Direct and indirect readout in mutant Met repressor-operator complexes.
Authors: Garvie, C.W. / Phillips, S.E.
History
DepositionJan 30, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 2, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HALF CONSENSUS DNA OPERATOR DUPLEX
D: HALF CONSENSUS DNA OPERATOR DUPLEX
A: METHIONINE REPRESSOR
B: METHIONINE REPRESSOR


Theoretical massNumber of molelcules
Total (without water)30,1474
Polymers30,1474
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.960, 64.000, 114.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain HALF CONSENSUS DNA OPERATOR DUPLEX


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein METHIONINE REPRESSOR


Mass: 12028.607 Da / Num. of mol.: 2 / Mutation: Q44K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: METJ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8U6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.44 Å3/Da / Density % sol: 50 %
Crystal growpH: 7
Details: PROTEIN (10MG/ML) + DNA (3.8MG/ML) WAS CRYSTALLISED FROM 8-14% P4000, 100MM CITRATE BUFFER, PH 5.0-6.0, 20% GLYCEROL, pH 7.0
Components of the solutions
IDNameCrystal-IDSol-ID
1PROTEIN11
2DNA11
3PEG 400011
4CITRATE BUFFER11
5GLYCEROL11
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
24 mg/ml1drop
31.5 mg/mlSAM1drop
420 mM1dropMgCl2
520 mM1dropCaCl2
610 mMsodium cacodylate1drop
720 mMsodium cacodylate1reservoir
828-38 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25.4 Å / Num. obs: 60504 / % possible obs: 89.8 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.217 / % possible all: 56.3

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.86refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMA

1cma


Resolution: 2.2→25.4 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.282 725 5.3 %RANDOM
Rwork0.227 ---
obs0.227 13755 88.6 %-
Displacement parametersBiso mean: 28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 404 0 177 2271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.25 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.339 32 3.2 %
Rwork0.363 505 -
obs--53.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION4PARAMETER.ELEMENTSTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.86 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31

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