[English] 日本語
Yorodumi
- PDB-9cbr: Methionine synthase from Thermus thermophilus HB8, Homocysteine, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cbr
TitleMethionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)
ComponentsMethionine synthase
KeywordsTRANSFERASE / Methyl transferase / cobalamin-dependent / cobalamin binding / one-carbon metabolism
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / zinc ion binding / cytosol
Similarity search - Function
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 ...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
Similarity search - Domain/homology
COBALAMIN / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / : / Methionine synthase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsYamada, K. / Menjdoza, J. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1945174 United States
CitationJournal: To Be Published
Title: Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)
Authors: Menjdoza, J. / Yamada, K. / Koutmos, M.
History
DepositionJun 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2906
Polymers95,3301
Non-polymers1,9605
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.811, 115.101, 120.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Methionine synthase / 5-methyltetrahydrofolate--homocysteine methyltransferase


Mass: 95330.180 Da / Num. of mol.: 1
Mutation: F110A, E123A, E124A, R268A, N283G, D651A, P652A, G653A, D759A, N774H, R826A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0618 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKM5, methionine synthase

-
Non-polymers , 5 types, 246 molecules

#2: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% PEG 3350, 0.1 M Tris (pH 8.5), and 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2022
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing, with two horizontally deflecting mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.38→120.79 Å / Num. obs: 39748 / % possible obs: 98.8 % / Redundancy: 5.6 % / CC1/2: 0.908 / Rmerge(I) obs: 0.549 / Rpim(I) all: 0.251 / Rrim(I) all: 0.605 / Χ2: 1.05 / Net I/σ(I): 3.8 / Num. measured all: 222476
Reflection shellResolution: 2.38→2.47 Å / % possible obs: 89.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 4.166 / Num. measured all: 19913 / Num. unique obs: 3707 / CC1/2: 0.221 / Rpim(I) all: 1.922 / Rrim(I) all: 4.604 / Χ2: 0.28 / Net I/σ(I) obs: 0.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→83.33 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.869 / SU B: 7.694 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24839 2019 5.1 %RANDOM
Rwork0.23645 ---
obs0.23707 37675 88.04 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.515 Å2
Baniso -1Baniso -2Baniso -3
1--22.03 Å2-0 Å2-0 Å2
2--11.71 Å20 Å2
3---10.32 Å2
Refinement stepCycle: 1 / Resolution: 2.38→83.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 127 242 7011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166767
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.8859385
X-RAY DIFFRACTIONr_angle_other_deg0.5931.76315551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.186562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.528101167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021516
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1611.9023470
X-RAY DIFFRACTIONr_mcbond_other1.161.9023471
X-RAY DIFFRACTIONr_mcangle_it1.8863.4364334
X-RAY DIFFRACTIONr_mcangle_other1.8863.4364335
X-RAY DIFFRACTIONr_scbond_it1.0811.9673442
X-RAY DIFFRACTIONr_scbond_other1.0811.9673443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7313.5855052
X-RAY DIFFRACTIONr_long_range_B_refined4.61522.628993
X-RAY DIFFRACTIONr_long_range_B_other4.59422.5728924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.383→2.445 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 95 -
Rwork0.388 2417 -
obs--85.62 %
Refinement TLS params.Method: refined / Origin x: 8.163 Å / Origin y: -19.513 Å / Origin z: -18.645 Å
111213212223313233
T0.0492 Å2-0.025 Å20.0026 Å2-0.1886 Å20.0036 Å2--0.0582 Å2
L0.4414 °2-0.6047 °2-0.0929 °2-1.1438 °20.1152 °2--0.2518 °2
S0.0359 Å °0.0673 Å °0.1126 Å °-0.0661 Å °0.0142 Å °-0.1621 Å °-0.0041 Å °-0.0143 Å °-0.0501 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 872
2X-RAY DIFFRACTION1A901 - 905

+
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