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- PDB-1mjk: METHIONINE REPRESSOR MUTANT APOREPRESSOR (Q44K) FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1mjk
TitleMETHIONINE REPRESSOR MUTANT APOREPRESSOR (Q44K) FROM ESCHERICHIA COLI
ComponentsMETHIONINE REPRESSOR
KeywordsTRANSCRIPTION REGULATION / METJ / REPRESSOR / SHEET-HELIX-HELIX
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
PHOSPHATE ION / Met repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER METHODS / Resolution: 2.15 Å
AuthorsGarvie, C.W. / Phillips, S.E.V.
CitationJournal: Thesis, University of Leeds / Year: 1997
Title: Crystallographic studies of the methionine repressor-operator complex and the oc31 42kDa repressor
Authors: Garvie, C.W.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHIONINE REPRESSOR
B: METHIONINE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1523
Polymers24,0572
Non-polymers951
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-46 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.680, 63.570, 44.610
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.06 Å3/Da / Density % sol: 40 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 16-28% PEG 600, 1.5% NAIO4, 100MM POTASSIUM PHOSPHATE BUFFER, PH 7.0.
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→23 Å / Num. obs: 10414 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.205 / % possible all: 87.6

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Processing

Software
NameVersionClassification
X-PLOR3.84model building
X-PLOR3.84refinement
XDSdata reduction
CCP4data scaling
X-PLOR3.84phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER METHODS
Starting model: PDB ENTRY 1CMB

1cmb


Resolution: 2.15→23 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 959 9.9 %RANDOM
Rwork0.181 ---
obs0.181 10402 97.5 %-
Displacement parametersBiso mean: 30.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.15→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 5 112 1807
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.33
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: 2.15→2.23 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 84 10.8 %
Rwork0.23 694 -
obs--72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
Refinement
*PLUS
Rfactor Rfree: 0.223 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33
LS refinement shell
*PLUS
Rfactor Rfree: 0.293 / Rfactor Rwork: 0.23

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