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- PDB-1cmb: THREE DIMENSIONAL CRYSTAL STRUCTURES OF ESCHERICHIA COLI MET REPR... -

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Basic information

Entry
Database: PDB / ID: 1cmb
TitleTHREE DIMENSIONAL CRYSTAL STRUCTURES OF ESCHERICHIA COLI MET REPRESSOR WITH AND WITHOUT COREPRESSOR
ComponentsMET APO-REPRESSOR
KeywordsDNA-BINDING REGULATORY PROTEIN
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 / Resolution: 1.8 Å
AuthorsRafferty, J.B. / Phillips, K. / Phillips, S.E.V.
CitationJournal: Nature / Year: 1989
Title: Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor.
Authors: Rafferty, J.B. / Somers, W.S. / Saint-Girons, I. / Phillips, S.E.
History
DepositionAug 28, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: MET APO-REPRESSOR
B: MET APO-REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1503
Polymers24,0552
Non-polymers951
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-45 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.600, 62.600, 44.500
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MET APO-REPRESSOR


Mass: 12027.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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.: 88 / Source method: isolated from a natural source / Formula: H2O
Compound detailsONE OF THE FLEXIBLE HAIRPIN LOOPS 12B - 20B IS SEVERELY DISORDERED. THE CONFORMATION IN THE ...ONE OF THE FLEXIBLE HAIRPIN LOOPS 12B - 20B IS SEVERELY DISORDERED. THE CONFORMATION IN THE COORDINATES IS POOR, BUT PROBABLY APPROXIMATES TO A MAJOR COMPONENT. THE LOOP IS UNLIKE THE EQUIVALENT ONE (12A - 20A) IN THE FIRST SUBUNIT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7 / Details: referred to J.Mol.Biol. 200.217-219 1988
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2200 mg/mlPEG6001reservoir
30.1 M1reservoirNaKPO4
40.1 Macetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.186 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 5 88 1783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 3 / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 5.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_plane_restr0.011

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