[English] 日本語
Yorodumi
- PDB-6bm5: Crystal Structure of the MetH Reactivation Domain bound to AdoMet -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bm5
TitleCrystal Structure of the MetH Reactivation Domain bound to AdoMet
ComponentsMethionine synthase
KeywordsTRANSFERASE / C-terminal domain / reactivation domain / MetH-AdoMet / MetH-SAM
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methylation / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily ...Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / : / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Methionine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsFick, R.J. / Vander Lee, L.P. / Trievel, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1508492 United States
CitationJournal: Biochemistry / Year: 2018
Title: Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.
Authors: Fick, R.J. / Clay, M.C. / Vander Lee, L. / Scheiner, S. / Al-Hashimi, H. / Trievel, R.C.
History
DepositionNov 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2922
Polymers37,8931
Non-polymers3981
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.098, 61.669, 139.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Methionine synthase / 5-methyltetrahydrofolate--homocysteine methyltransferase / Methionine synthase / vitamin-B12-dependent / MS


Mass: 37893.293 Da / Num. of mol.: 1 / Fragment: reactivation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: metH, b4019, JW3979 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P13009, methionine synthase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.17 Å3/Da / Density % sol: 43.29 % / Mosaicity: 0.423 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 28% PEG 6000, 100mM Tris pH 7.4, 300mM magnesium acetate:15mg/mL protein, 3mM AdoMet, 10mM Tris 7.2, 10mM EDTA, 3:3uL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 53119 / % possible obs: 98.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.88 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.028 / Rrim(I) all: 0.067 / Χ2: 0.98 / Net I/σ(I): 12.8 / Num. measured all: 285503
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.533.70.23323670.9620.1290.2680.89688.8
1.53-1.5540.21924740.970.1170.2490.85594.5
1.55-1.584.50.19125840.9810.0960.2150.89196.4
1.58-1.625.20.18526060.9850.0870.2050.88798.6
1.62-1.655.30.16926510.9880.0790.1870.88999.6
1.65-1.695.50.15126380.990.0690.1660.89799.8
1.69-1.735.60.13226660.9920.0610.1460.90499.9
1.73-1.785.70.11926430.9920.0550.1321.007100
1.78-1.835.70.10726890.9940.0490.1181.052100
1.83-1.895.70.09526550.9950.0430.1051.0899.8
1.89-1.965.70.0926670.9940.0410.0991.03199.9
1.96-2.045.60.0826860.9960.0370.0890.96599.9
2.04-2.135.70.07327040.9960.0330.0811.005100
2.13-2.245.70.06726630.9970.030.0731.02199.9
2.24-2.385.80.06527000.9970.0290.0711.046100
2.38-2.565.70.06127070.9970.0280.0671.04299.9
2.56-2.825.70.05827060.9970.0270.0641.025100
2.82-3.235.60.05427570.9970.0250.0590.95499.9
3.23-4.075.60.04727690.9970.0210.0520.94199.7
4.07-505.30.04327870.9970.020.0481.06994.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.36 Å37.2 Å
Translation5.36 Å37.2 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.6.0phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1MSK

1msk


Resolution: 1.5→37.199 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.11
RfactorNum. reflection% reflection
Rfree0.1935 2651 5 %
Rwork0.1459 --
obs0.1482 53031 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.96 Å2 / Biso mean: 23.3677 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: final / Resolution: 1.5→37.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 27 484 3068
Biso mean--19.1 34.34 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072694
X-RAY DIFFRACTIONf_angle_d0.8993684
X-RAY DIFFRACTIONf_chiral_restr0.082391
X-RAY DIFFRACTIONf_plane_restr0.006484
X-RAY DIFFRACTIONf_dihedral_angle_d5.4631534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4943-1.52140.2365950.18081812190767
1.5214-1.55070.22691340.16472533266795
1.5507-1.58240.18961360.14742601273796
1.5824-1.61680.21021400.1432644278499
1.6168-1.65440.23221420.140726982840100
1.6544-1.69570.20581380.134426612799100
1.6957-1.74160.20111410.133626862827100
1.7416-1.79280.17211420.131726782820100
1.7928-1.85070.20811420.135927092851100
1.8507-1.91690.19491420.148826962838100
1.9169-1.99360.19631420.145426982840100
1.9936-2.08430.17591420.143926982840100
2.0843-2.19420.1791440.138527142858100
2.1942-2.33170.17831430.138827172860100
2.3317-2.51160.18021430.151327402883100
2.5116-2.76430.19871440.163527312875100
2.7643-3.16420.22411470.161127902937100
3.1642-3.98580.18091460.134927662912100
3.9858-37.21080.19031480.14622808295695

+
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