[English] 日本語
Yorodumi
- PDB-1cma: MET REPRESSOR/DNA COMPLEX + S-ADENOSYL-METHIONINE -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / S-Adenosyl methionine


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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
6NACLSodium chloride11
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more