[English] 日本語
Yorodumi
- PDB-9xsa: Crystal structure of a cupin protein (tm1459, R39M/H52A/H54A/H92A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9xsa
TitleCrystal structure of a cupin protein (tm1459, R39M/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form
ComponentsCupin type-2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzymes / Biocatalysis / Ruthenium(p-cymene)
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / 1-methyl-4-(1-methylethyl)benzene / RUTHENIUM ION / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.423 Å
AuthorsMatsumoto, K. / Matsumoto, R. / Morita, Y. / Fujieda, N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JSPS KAKENHI Grant Number 21H01954 Japan
Japan Society for the Promotion of Science (JSPS)JSPS KAKENHI Grant Number 24K01503 Japan
Japan Society for the Promotion of Science (JSPS)JSPS KAKENHI Grant Number 25H02285 Japan
CitationJournal: Chem.Commun.(Camb.) / Year: 2026
Title: Rational design of a ruthenium-cupin complex as an artificial ketone reductase.
Authors: Matsumoto, K. / Kitazawa, S. / Matsumoto, R. / Morita, Y. / Fujieda, N.
History
DepositionNov 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cupin type-2 domain-containing protein
B: Cupin type-2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9236
Polymers26,4522
Non-polymers4714
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-33 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.197, 57.755, 75.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cupin type-2 domain-containing protein


Mass: 13226.135 Da / Num. of mol.: 2 / Mutation: R39M/H52A/H54A/H92A/C106E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Gene: TM_1459, Tmari_1465 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1H0
#2: Chemical ChemComp-MML / 1-methyl-4-(1-methylethyl)benzene / p-cymene


Mass: 134.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14
#3: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ru
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25% w/v Jeffamine ED-2001, 0.1M MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.899995 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899995 Å / Relative weight: 1
ReflectionResolution: 1.423→50 Å / Num. obs: 78202 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.15
Reflection shellResolution: 1.423→1.51 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 12504 / CC1/2: 0.732 / % possible all: 97.8

-
Processing

Software
NameClassification
SHELXLrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.423→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 3925 5 %RANDOM
Rwork0.1884 ---
all0.1915 ---
obs0.1915 78202 99 %-
Refinement stepCycle: LAST / Resolution: 1.423→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 0 121 1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONs_bond_d0.00691831
X-RAY DIFFRACTIONs_angle_d0.01962521
X-RAY DIFFRACTIONs_similar_dist00
X-RAY DIFFRACTIONs_from_restr_planes0.4249584
X-RAY DIFFRACTIONs_zero_chiral_vol0.0803295
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.5973280
X-RAY DIFFRACTIONs_anti_bump_dis_restr00
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.047212901
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.071210884
X-RAY DIFFRACTIONs_approx_iso_adps00
LS refinement shellResolution: 1.423→1.48 Å /
RfactorNum. reflection
Rwork0.284 7972

+
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