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- PDB-8hjy: Crystal structure of a cupin protein (tm1459, H52A/H58E/F104W mut... -

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Basic information

Entry
Database: PDB / ID: 8hjy
TitleCrystal structure of a cupin protein (tm1459, H52A/H58E/F104W mutant) in copper (Cu) substituted form
ComponentsCupin_2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzymes / Non-heme copper enzyme / Cupin
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 MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsMatsumoto, R. / Kurisu, G. / Fujieda, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H04270 Japan
Japan Society for the Promotion of Science (JSPS)21H01954 Japan
Citation
Journal: Chem Sci / Year: 2023
Title: An artificial metallolyase with pliable 2-His-1-carboxylate facial triad for stereoselective Michael addition.
Authors: Matsumoto, R. / Yoshioka, S. / Yuasa, M. / Morita, Y. / Kurisu, G. / Fujieda, N.
#1: Journal: Chem Sci / Year: 2023
Title: An artificial metallolyase with pliable 2-His-1-carboxylate facial triad for stereoselective Michael addition.
Authors: Matsumoto, R. / Yoshioka, S. / Yuasa, M. / Morita, Y. / Kurisu, G. / Fujieda, N.
History
DepositionNov 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cupin_2 domain-containing protein
B: Cupin_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9715
Polymers26,7812
Non-polymers1913
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-62 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.700, 57.720, 75.820
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_2 domain-containing protein


Mass: 13390.303 Da / Num. of mol.: 2 / Mutation: H52A/H58E/F104W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1459 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1H0
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% w/v Jeffamine ED-2001, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.18→99 Å / Num. obs: 141051 / % possible obs: 99 % / Redundancy: 3.45 % / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.78
Reflection shellResolution: 1.18→1.25 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 22674 / CC1/2: 0.706 / % possible all: 98.4

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Processing

Software
NameVersionClassification
SHELXL2017/01refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L2E

6l2e


Resolution: 1.18→99 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 7082 5 %RANDOM
Rwork0.1522 ---
all0.1925 ---
obs-141043 99.1 %-
Refinement stepCycle: LAST / Resolution: 1.18→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 3 217 2123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0114
X-RAY DIFFRACTIONs_angle_d0.0281
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.3811
X-RAY DIFFRACTIONs_zero_chiral_vol0.0937
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.7048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0359
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0.158
LS refinement shellResolution: 1.18→1.22 Å / Rfactor Rwork: 0.272

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