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- PDB-1cmc: THREE DIMENSIONAL CRYSTAL STRUCTURES OF E. COLI MET REPRESSOR WIT... -

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Basic information

Entry
Database: PDB / ID: 1cmc
TitleTHREE DIMENSIONAL CRYSTAL STRUCTURES OF E. COLI MET REPRESSOR WITH AND WITHOUT COREPRESSOR
ComponentsMET 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
S-ADENOSYLMETHIONINE / Met repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSomers, W.S. / 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 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,9016
Polymers24,0552
Non-polymers8454
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-46 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.070, 75.070, 81.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: THE IDENTITY OF RESIDUES 106 A AND 106 B IS UNKNOWN. EACH INTERACTS WITH HIS 14, GLU 19, A SYMMETRY RELATED GLU 103, AND THE C-TERMINUS. THE MAGNITUDE OF THE DENSITY PEAK SUGGESTS ATOMIC NUMBER IN ...1: THE IDENTITY OF RESIDUES 106 A AND 106 B IS UNKNOWN. EACH INTERACTS WITH HIS 14, GLU 19, A SYMMETRY RELATED GLU 103, AND THE C-TERMINUS. THE MAGNITUDE OF THE DENSITY PEAK SUGGESTS ATOMIC NUMBER IN RANGE 25 - 35. IT IS POSSIBLY ARSENIC FROM BUFFER. IN REFINEMENT IT WAS MODELLED BY A MAGNESIUM ION WITH OCCUPANCY 2.0.

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Components

#1: Protein MET 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE IDENTITY OF RESIDUES 106 A AND 106 B IS UNKNOWN. EACH INTERACTS WITH HIS 14, GLU 19, A SYMMETRY ...THE IDENTITY OF RESIDUES 106 A AND 106 B IS UNKNOWN. EACH INTERACTS WITH HIS 14, GLU 19, A SYMMETRY RELATED GLU 103, AND THE C-TERMINUS. THE MAGNITUDE OF THE DENSITY PEAK SUGGESTS ATOMIC NUMBER IN RANGE 25 - 35. IT IS POSSIBLY ARSENIC FROM BUFFER. IN REFINEMENT IT WAS MODELLED BY A MAGNESIUM ION WITH OCCUPANCY 2.0.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal grow
*PLUS
Method: microdialysis / pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
115 mg/ml1Mg2+2
22.5 mMSAM12
310 mMNa cacodylate12

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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: 0.183 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 56 206 1952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
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: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 6.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.054
X-RAY DIFFRACTIONp_plane_restr0.018

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