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- PDB-9xs8: Crystal structure of a cupin protein (tm1459, H52A/H54A/H92A/C106... -

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Basic information

Entry
Database: PDB / ID: 9xs8
TitleCrystal structure of a cupin protein (tm1459, 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: 1.265 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)27,0366
Polymers26,5042
Non-polymers5324
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-27 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.810, 57.630, 74.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13252.133 Da / Num. of mol.: 2 / Mutation: 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.: 1 / Source method: obtained synthetically / Formula: C10H14
#3: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ru
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25% w/v Jeffamine ED-2001, 0.1M MES

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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 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899995 Å / Relative weight: 1
ReflectionResolution: 1.265→50 Å / Num. obs: 112232 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.79
Reflection shellResolution: 1.265→1.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 18121 / CC1/2: 0.723 / % possible all: 98.9

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Processing

Software
NameClassification
SHELXLrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.265→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 5607 5 %RANDOM
Rwork0.1474 ---
all0.1487 ---
obs0.1487 112232 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.265→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 0 211 3852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONs_bond_d0.00981887
X-RAY DIFFRACTIONs_angle_d0.02572572
X-RAY DIFFRACTIONs_similar_dist00
X-RAY DIFFRACTIONs_from_restr_planes0.433591
X-RAY DIFFRACTIONs_zero_chiral_vol0.098309
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.6706281
X-RAY DIFFRACTIONs_anti_bump_dis_restr00
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.040113310
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065211418
X-RAY DIFFRACTIONs_approx_iso_adps0.16651248
LS refinement shellResolution: 1.265→1.31 Å /
RfactorNum. reflection
Rwork0.262 11058

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