[English] 日本語
Yorodumi
- PDB-1j6r: Crystal structure of Activation (AdoMet binding) domain of Methio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j6r
TitleCrystal structure of Activation (AdoMet binding) domain of Methionine synthase (TM0269) from Thermotoga maritima at 2.2 A resolution
ComponentsMETHIONINE SYNTHASE
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / TM0269 / ACTIVATION (ADOMET BINDING) DOMAIN OF METHIONINE SYNTHASE / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homologyNADH Oxidase - #40 / S-adenosyl-L-methionine dependent methionine synthase, predicted / Vitamin B12-dependent methionine synthase, activation domain superfamily / methionine synthase activity / NADH Oxidase / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Activation (AdoMet binding) domain of Methionine synthase (TM0269) from Thermotoga maritima at 2.2 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Jan 25, 2023Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHIONINE SYNTHASE
B: METHIONINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)48,7682
Polymers48,7682
Non-polymers00
Water1,856103
1
A: METHIONINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)24,3841
Polymers24,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METHIONINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)24,3841
Polymers24,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.396, 60.740, 81.574
Angle α, β, γ (deg.)90.00, 99.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein METHIONINE SYNTHASE /


Mass: 24383.975 Da / Num. of mol.: 2 / Fragment: ACTIVATION (ADOMET BINDING) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0269 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYA6, methionine synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 293 K / pH: 7
Details: 2.4 M Ammonium Sulfate; 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 7.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.979029
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9790291
ReflectionResolution: 2.25→36.22 Å / Num. obs: 27922 / % possible obs: 90.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 43.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 14
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.344 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
RESOLVEmodel building
CNSrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→36.22 Å / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
Details: DISORDERED SIDECHAINS: CHAIN A: 45, 52,72,76,154,170, 179,180,181,197; CHAIN B: 30,31,34,45,52,72, 76, 86,145,154,163,164,170,178,181,197 DISORDERED RESIDUES: CHAIN A: 177,178 CHAIN B: ...Details: DISORDERED SIDECHAINS: CHAIN A: 45, 52,72,76,154,170, 179,180,181,197; CHAIN B: 30,31,34,45,52,72, 76, 86,145,154,163,164,170,178,181,197 DISORDERED RESIDUES: CHAIN A: 177,178 CHAIN B: 179,180. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1500 5.1 %RANDOM
Rwork0.251 ---
obs0.251 27922 99.9 %-
Solvent computationSolvent model: BULK SOLVENT MODELLING / Bsol: 322.79 Å2 / ksol: 0.9 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.33 Å2
2--2.81 Å20 Å2
3----1.75 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 0 103 3249
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4171.5
X-RAY DIFFRACTIONc_mcangle_it2.5272
X-RAY DIFFRACTIONc_scbond_it1.2522
X-RAY DIFFRACTIONc_scangle_it2.2012.5
LS refinement shellResolution: 2.3→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 119 5 %
Rwork0.325 2076 -
obs--96 %

+
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