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- PDB-5wsd: Crystal structure of a cupin protein (tm1459) in apo form -

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Basic information

Entry
Database: PDB / ID: 5wsd
TitleCrystal structure of a cupin protein (tm1459) in apo form
ComponentsUncharacterized protein tm1459
KeywordsMETAL BINDING PROTEIN / cupin fold / artificial metalloenzyme / metal binding / 4 histidine motif
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupin type-2 domain-containing protein / Cupin type-2 domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFujieda, N. / Nakano, T. / Taniguchi, Y. / Ichihashi, H. / Nishikawa, Y. / Kurisu, G. / Itoh, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and TechnologyJP15H01066 Japan
Ministry of Education, Culture, Sports, Science and TechnologyJP16H01025 Japan
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: A Well-Defined Osmium-Cupin Complex: Hyperstable Artificial Osmium Peroxygenase
Authors: Fujieda, N. / Nakano, T. / Taniguchi, Y. / Ichihashi, H. / Sugimoto, H. / Morimoto, Y. / Nishikawa, Y. / Kurisu, G. / Itoh, S.
History
DepositionDec 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein tm1459
B: Uncharacterized protein tm1459


Theoretical massNumber of molelcules
Total (without water)26,9192
Polymers26,9192
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-33 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.587, 57.591, 74.643
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 Uncharacterized protein tm1459


Mass: 13459.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1459, Tmari_1465 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1H0, UniProt: R4P0Z5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% Jeffamine ED-2001, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 68873 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.5
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3325 / CC1/2: 0.721 / % possible all: 98.8

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Processing

Software
NameClassification
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SHELXL-97refinement
SHELXLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vj2

1vj2


Resolution: 1.2→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3446 5 %RANDOM
Rwork0.1575 ---
obs0.1578 64882 100 %-
Refine analyzeNum. disordered residues: 133 / Occupancy sum non hydrogen: 2084.4
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 16 328 2280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.004
X-RAY DIFFRACTIONs_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.705
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.028
X-RAY DIFFRACTIONs_approx_iso_adps0.133

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