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- PDB-3bk6: Crystal structure of a core domain of stomatin from Pyrococcus ho... -

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Basic information

Entry
Database: PDB / ID: 3bk6
TitleCrystal structure of a core domain of stomatin from Pyrococcus horikoshii
ComponentsPH stomatin
KeywordsMEMBRANE PROTEIN / stomatin / archaea / Pyrococcus horikoshii / trimer / coiled-coil / flotillin / SPFH / membrane fusion / trafficking / Transmembrane
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2090 / Band 7 domain / Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Tetrahydropterin Synthase; Chain A / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2090 / Band 7 domain / Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Tetrahydropterin Synthase; Chain A / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Stomatin homolog PH1511
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsYokoyama, H. / Fujii, S. / Matsui, I.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of a core domain of stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold
Authors: Yokoyama, H. / Fujii, S. / Matsui, I.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii
Authors: Yokoyama, H. / Matsui, E. / Akiba, T. / Harata, K. / Matsui, I.
History
DepositionDec 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PH stomatin
B: PH stomatin
C: PH stomatin


Theoretical massNumber of molelcules
Total (without water)63,8923
Polymers63,8923
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.553, 137.150, 58.544
Angle α, β, γ (deg.)90.00, 107.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PH stomatin / P-STOMATIN PH1511


Mass: 21297.398 Da / Num. of mol.: 3 / Fragment: Residues 56-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1511 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: O59180

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% MPD, 0.2M ammonium sulfate, 0.1M HEPES-NaOH, 6% 1,5-diaminopentane-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9791, 0.9796, 0.9900, 1.0000
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Nov 24, 2005 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97961
30.991
411
ReflectionResolution: 3.2→50 Å / Num. obs: 17735 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 114.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 33.5
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→19.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 18.023 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 1.343 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26234 1792 10.2 %RANDOM
Rwork0.19774 ---
obs0.20446 15824 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.114 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 0 0 3732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223770
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.975105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7325469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5124.514175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.54715728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7561538
X-RAY DIFFRACTIONr_chiral_restr0.1240.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022756
X-RAY DIFFRACTIONr_nbd_refined0.2820.21735
X-RAY DIFFRACTIONr_nbtor_refined0.330.22551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.25
X-RAY DIFFRACTIONr_mcbond_it3.83622455
X-RAY DIFFRACTIONr_mcangle_it5.88933865
X-RAY DIFFRACTIONr_scbond_it4.39321468
X-RAY DIFFRACTIONr_scangle_it7.17331240
LS refinement shellResolution: 3.201→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 117 -
Rwork0.294 1120 -
obs--96.34 %

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