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- PDB-3wg5: 1510-N membrane-bound stomatin-specific protease K138A mutant in ... -

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Basic information

Entry
Database: PDB / ID: 3wg5
Title1510-N membrane-bound stomatin-specific protease K138A mutant in complex with a substrate peptide under heat treatment
Components
  • 441aa long hypothetical nfeD protein
  • PH1511 stomatin
KeywordsHYDROLASE/PROTEIN BINDING / protein-peptide complex / alpha/beta motif / protease / membrane protein stomatin / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / membrane / plasma membrane
Similarity search - Function
Archaeal protein PH0471, N-terminal / Band-7 stomatin-like / NfeD-like, C-terminal domain / Band 7/stomatin-like, conserved site / NfeD-like C-terminal, partner-binding / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues ...Archaeal protein PH0471, N-terminal / Band-7 stomatin-like / NfeD-like, C-terminal domain / Band 7/stomatin-like, conserved site / NfeD-like C-terminal, partner-binding / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Membrane-bound protease PH1510 / Stomatin homolog PH1511
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
Pyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYokoyama, H. / Fujii, S. / Matsui, I.
Citation
Journal: J.Synchrotron Radiat. / Year: 2013
Title: Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease.
Authors: Yokoyama, H. / Kobayashi, D. / Takizawa, N. / Fujii, S. / Matsui, I.
#1: Journal: Biochemistry / Year: 2012
Title: Crystal structure of a membrane stomatin-specific protease in complex with a substrate peptide
Authors: Yokoyama, H. / Takizawa, N. / Kobayashi, D. / Matsui, I. / Fujii, S.
History
DepositionJul 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 441aa long hypothetical nfeD protein
B: 441aa long hypothetical nfeD protein
C: PH1511 stomatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3219
Polymers51,8953
Non-polymers4276
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-22 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.448, 111.448, 91.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-304-

CL

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein 441aa long hypothetical nfeD protein / 1510-N membrane protease


Mass: 25368.025 Da / Num. of mol.: 2 / Fragment: UNP Residues 16-236 / Mutation: K138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1510 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: O59179
#2: Protein/peptide PH1511 stomatin / Uncharacterized protein PH1511


Mass: 1158.473 Da / Num. of mol.: 1 / Fragment: UNP Residues 234-243 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Pyrococcus horikoshii OT3 (archaea) / References: UniProt: O59180

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Non-polymers , 4 types, 146 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 19, 2011 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 23169 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 61.9
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 7.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VIV

3viv


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 15.089 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24082 2347 10.2 %RANDOM
Rwork0.20154 ---
obs0.20554 20752 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 28 140 3603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9854776
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01224.82139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96315602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9341516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212597
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7844.0491781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9366.0542221
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3174.3071738
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.82134.3475365
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 163 -
Rwork0.239 1489 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.15490.95860.21651.7461-0.53551.2973-0.2233-0.0014-0.2234-0.12590.1226-0.2007-0.0962-0.1360.10070.163-0.00120.0770.08780.02880.103725.33654.674719.0322
21.6451-0.0703-0.56991.18450.18211.9952-0.1502-0.25560.2701-0.36270.16180.1133-0.01340.0235-0.01160.2065-0.0463-0.04670.0701-0.03450.063926.01742.662520.5318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 237
2X-RAY DIFFRACTION1A301 - 304
3X-RAY DIFFRACTION2B19 - 237
4X-RAY DIFFRACTION2B301 - 302

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