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- PDB-21ek: Crystal structure of a cupin protein (tm1459, presequence-truncat... -

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Basic information

Entry
Database: PDB / ID: 21ek
TitleCrystal structure of a cupin protein (tm1459, presequence-truncated H52A mutant) soaked in CuSO4
ComponentsCupin type-2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzymes / Biocatalysis / Non-heme copper enzymes
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / COPPER (II) ION / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.162 Å
AuthorsMorikawa, S. / Saegusa, N. / 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: Chemcatchem / Year: 2026
Title: Structure-Guided Surface Engineering of an Artificial Metallolyase for Highly Enantioselective Michael Addition
Authors: Morikawa, S. / Saegusa, N. / Matsumoto, R. / Morita, Y. / Fujieda, N.
History
DepositionDec 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1582
Polymers13,0941
Non-polymers641
Water2,666148
1
A: Cupin type-2 domain-containing protein
hetero molecules

A: Cupin type-2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3154
Polymers26,1882
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3890 Å2
ΔGint-52 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.215, 52.215, 98.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

21A-398-

HOH

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Components

#1: Protein Cupin type-2 domain-containing protein / Cupin_2 domain-containing protein


Mass: 13094.003 Da / Num. of mol.: 1 / Mutation: H52A
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.37 %
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: Jun 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899995 Å / Relative weight: 1
ReflectionResolution: 1.162→45.22 Å / Num. obs: 103335 / % possible obs: 100 % / Redundancy: 5.11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 18.46
Reflection shellResolution: 1.162→1.23 Å / Redundancy: 4.88 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 16669 / CC1/2: 0.78 / % possible all: 99.9

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Processing

Software
NameClassification
PHASERphasing
SHELXLrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.162→45.22 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1727 5182 5 %RANDOM
Rwork0.146 ---
all0.1473 ---
obs0.1473 98153 100 %-
Refinement stepCycle: LAST / Resolution: 1.162→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 9 153 1082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONs_bond_d0.0119951
X-RAY DIFFRACTIONs_angle_d0.02471288
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.4204310
X-RAY DIFFRACTIONs_zero_chiral_vol0.1084153
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0765145
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.03256759
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.17055994
X-RAY DIFFRACTIONs_approx_iso_adps0894
LS refinement shellResolution: 1.162→1.2 Å / Rfactor Rwork: 0.235

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