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- PDB-5wse: Crystal structure of a cupin protein (tm1459) in osmium (Os) subs... -

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Basic information

Entry
Database: PDB / ID: 5wse
TitleCrystal structure of a cupin protein (tm1459) in osmium (Os) substituted form I
ComponentsUncharacterized protein tm1459
KeywordsMETAL BINDING PROTEIN / cupin fold / artificial metalloenzyme / metal binding / 4 histidine motif / Osmium / Os / Platinum group metal
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
OSMIUM ION / 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: 1.12 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein tm1459
B: Uncharacterized protein tm1459
C: Uncharacterized protein tm1459
D: Uncharacterized protein tm1459
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5988
Polymers53,8374
Non-polymers7614
Water8,035446
1
A: Uncharacterized protein tm1459
D: Uncharacterized protein tm1459
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2994
Polymers26,9192
Non-polymers3802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-47 kcal/mol
Surface area9750 Å2
MethodPISA
2
B: Uncharacterized protein tm1459
C: Uncharacterized protein tm1459
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2994
Polymers26,9192
Non-polymers3802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-46 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.396, 48.878, 62.597
Angle α, β, γ (deg.)69.07, 87.95, 78.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein tm1459


Mass: 13459.369 Da / Num. of mol.: 4
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 (E. coli) / References: UniProt: Q9X1H0, UniProt: R4P0Z5*PLUS
#2: Chemical
ChemComp-OS / OSMIUM ION / Osmium


Mass: 190.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Os
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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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: 1.84 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% w/v polyethylene glycol 1500, 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: May 11, 2015
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: 147917 / % possible obs: 94.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.8
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.847 / % possible all: 91.8

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Processing

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

1vj2


Resolution: 1.12→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 7237 5 %RANDOM
Rwork0.1513 ---
obs0.1514 137888 94.8 %-
Refine analyzeNum. disordered residues: 169 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3943.2
Refinement stepCycle: LAST / Resolution: 1.12→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3718 0 36 520 4274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0046
X-RAY DIFFRACTIONs_angle_d0.0159
X-RAY DIFFRACTIONs_from_restr_planes0.0013
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.54
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0135
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0181
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0286
X-RAY DIFFRACTIONs_approx_iso_adps0.0673
LS refinement shellHighest resolution: 1.12 Å /
RfactorNum. reflection
obs0.213 -
all-6858

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