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- PDB-9jev: Crystal structure of a cupin protein (tm1459) in zinc (Zn) substi... -

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Basic information

Entry
Database: PDB / ID: 9jev
TitleCrystal structure of a cupin protein (tm1459) in zinc (Zn) substituted form
ComponentsCupin type-2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Cupin
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsFujieda, N. / Ichihashi, H. / Kurisu, G. / Itoh, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JSPS KAKENHI 21H01954 Japan
CitationJournal: Chem Asian J / Year: 2025
Title: Unusual Self-Hydroxylation in 4-Histidine Tetrad-Supporting Nonheme Iron Center.
Authors: Fujieda, N. / Ishihama, K.I. / Ichihashi, H. / Yanagisawa, S. / Kurisu, G. / Itoh, S.
History
DepositionSep 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: 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)27,0504
Polymers26,9192
Non-polymers1312
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-107 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.598, 57.871, 74.650
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: 13459.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1459 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1H0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25%(w/v) Jeffamine ED-2001, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 85007 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.76
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 7 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 4227 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WSD

5wsd


Resolution: 1.12→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 4251 5 %RANDOM
Rwork0.138 ---
all0.1388 ---
obs0.1388 84933 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.12→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 2 342 4067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0105
X-RAY DIFFRACTIONs_angle_d0.0248
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.4097
X-RAY DIFFRACTIONs_zero_chiral_vol0.0768
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.6639
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0251
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0444
X-RAY DIFFRACTIONs_approx_iso_adps0.1467
LS refinement shellResolution: 1.12→1.16 Å /
RfactorNum. reflection
Rwork0.211 8131

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