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- PDB-1cma: MET REPRESSOR/DNA COMPLEX + S-ADENOSYL-METHIONINE -

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Basic information

Entry
Database: PDB / ID: 1cma
TitleMET REPRESSOR/DNA COMPLEX + S-ADENOSYL-METHIONINE
Components
  • DNA (5'-D(*AP*GP*AP*CP*GP*TP*CP*TP*A)-3')
  • DNA (5'-D(*TP*TP*AP*GP*AP*CP*GP*TP*CP*T)-3')
  • PROTEIN (MET REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / 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
S-ADENOSYLMETHIONINE / DNA / Met repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSomers, W.S. / Phillips, S.E.V.
Citation
Journal: Nature / Year: 1992
Title: Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands.
Authors: Somers, W.S. / Phillips, S.E.
#1: Journal: 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.V.
History
DepositionAug 24, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
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

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*TP*AP*GP*AP*CP*GP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*CP*GP*TP*CP*TP*A)-3')
A: PROTEIN (MET REPRESSOR)
B: PROTEIN (MET REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6276
Polymers29,8304
Non-polymers7972
Water64936
1
C: DNA (5'-D(*TP*TP*AP*GP*AP*CP*GP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*CP*GP*TP*CP*TP*A)-3')
A: PROTEIN (MET REPRESSOR)
B: PROTEIN (MET REPRESSOR)
hetero molecules

C: DNA (5'-D(*TP*TP*AP*GP*AP*CP*GP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*CP*GP*TP*CP*TP*A)-3')
A: PROTEIN (MET REPRESSOR)
B: PROTEIN (MET REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,25412
Polymers59,6608
Non-polymers1,5944
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)121.350, 121.350, 84.810
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 DNA (5'-D(*TP*TP*AP*GP*AP*CP*GP*TP*CP*T)-3')


Mass: 3035.003 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*GP*AP*CP*GP*TP*CP*TP*A)-3')


Mass: 2739.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (MET REPRESSOR)


Mass: 12027.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A8U6
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.99 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4NA AZIDE11
5CACL211
6NACL11
7SAM11
8WATER12
9MPD12
10NA CACODYLATE12
11NA AZIDE12
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mloligonucleotide1drop
29 mg/mlprotein1drop
322 mMcalcium chloride1drop
410 mMsodium cacodylate1drop
56 mMsodium chloride1drop
61 mg/mlSAM1drop
710 mMsodium cacodylate1reservoir
81 mMsodium azaid1reservoir
935 %(v/v)1reservoir
101
111

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6
DetectorType: ARNDT-WONACOTT / Detector: OSCILLATION CAMERA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. obs: 8856
Reflection
*PLUS
Highest resolution: 2.8 Å / % possible obs: 97.7 % / Num. measured all: 33481 / Rmerge(I) obs: 0.074

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.8→10 Å /
RfactorNum. reflection
obs0.22 8856
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 386 54 36 2166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg1.68
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.007
X-RAY DIFFRACTIONt_it6.6
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1.68
X-RAY DIFFRACTIONt_plane_restr0.07

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