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- PDB-1mjp: METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO THE MINIMAL ME... -

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Basic information

Entry
Database: PDB / ID: 1mjp
TitleMETHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR
Components
  • (CONSENSUS OPERATOR DUPLEX) x 2
  • METHIONINE REPRESSOR
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / METJ / METHIONINE REPRESSOR / SHEET-HELIX-HELIX / SAM / S-ADENOSYL METHIONINE / 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 / DIFFERENCE FOURIER METHODS / Resolution: 3.4 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 29, 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 1.3Mar 14, 2018Group: Advisory / Database references / Category: pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Advisory / Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,8324
Polymers29,8324
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.390, 118.390, 83.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: DNA chain CONSENSUS OPERATOR DUPLEX


Mass: 3035.003 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain CONSENSUS OPERATOR DUPLEX


Mass: 2739.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: 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

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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: 2.82 Å3/Da / Density % sol: 56 %
Crystal growpH: 7
Details: PROTEIN (10MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 40% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 7.0.
Components of the solutions
IDNameCrystal-IDSol-ID
1PROTEIN11
2DNA11
3MPD11
4SODIUM CACODYLATE11
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 IIC / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 19851 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.5
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.231 / % possible all: 100

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.86refinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER METHODS
Starting model: PDB ENTRY 1CMA

1cma


Resolution: 3.4→30 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.309 480 9.9 %RANDOM
Rwork0.226 ---
obs0.226 4864 95.2 %-
Displacement parametersBiso mean: 72.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 382 0 0 2072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
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: 3.4→3.48 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.347 43 13.4 %
Rwork0.313 279 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.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_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

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