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- PDB-8gn9: SPFH domain of Pyrococcus horikoshii stomatin -

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Basic information

Entry
Database: PDB / ID: 8gn9
TitleSPFH domain of Pyrococcus horikoshii stomatin
ComponentsStomatin homolog PH1511
KeywordsMEMBRANE PROTEIN / mixed alpha-beta / dimer / scaffolding protein
Function / homology
Function and homology information


Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Stomatin homolog PH1511
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKomatsu, T. / Matsui, I. / Yokoyama, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K07316 Japan
CitationJournal: Biochem Biophys Rep / Year: 2022
Title: Structural and mutational studies suggest key residues to determine whether stomatin SPFH domains form dimers or trimers.
Authors: Komatsu, T. / Matsui, I. / Yokoyama, H.
History
DepositionAug 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stomatin homolog PH1511
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3062
Polymers12,2831
Non-polymers231
Water37821
1
A: Stomatin homolog PH1511
hetero molecules

A: Stomatin homolog PH1511
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6124
Polymers24,5662
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)28.014, 28.014, 240.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Stomatin homolog PH1511 / Prokaryotic stomatin / P-stomatin


Mass: 12283.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 63-170 / Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1511 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: O59180
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M sodium acetate, 50 mM Tris-HCl, 15% PEG4000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 3909 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 31.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 536 / CC1/2: 0.951 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bk6

3bk6


Resolution: 2.5→19.81 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.938 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 402 10.5 %RANDOM
Rwork0.2153 ---
obs0.2217 3443 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.89 Å2 / Biso mean: 43.406 Å2 / Biso min: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 2.5→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 1 21 862
Biso mean--34.37 38.88 -
Num. residues----106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.013850
X-RAY DIFFRACTIONr_bond_other_d0.0020.015858
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.6451159
X-RAY DIFFRACTIONr_angle_other_deg1.2081.5841969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1945105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53223.40944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98715158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.083156
X-RAY DIFFRACTIONr_chiral_restr0.0530.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02175
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 36 -
Rwork0.235 233 -
all-269 -
obs--100 %

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