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

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Basic information

Entry
Database: PDB / ID: 3viv
Title1510-N membrane-bound stomatin-specific protease K138A mutant in complex with a substrate peptide
Components
  • 441aa long hypothetical nfeD protein
  • PH STOMATIN PH1511
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 / : / : / NfeD integral membrane domain / NfeD1b, N-terminal domain / Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / NfeD-like, C-terminal domain / : ...Archaeal protein PH0471, N-terminal / : / : / NfeD integral membrane domain / NfeD1b, N-terminal domain / Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily / 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 / molecular replacement / Resolution: 2.25 Å
AuthorsYokoyama, H. / Matsui, I. / Fujii, S.
Citation
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.
#1: Journal: J.SYNCHROTRON RADIAT. / Year: 2008
Title: Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin.
Authors: Yokoyama, H. / Hamamatsu, S. / Fujii, S. / Matsui, I.
#2: 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
DepositionOct 12, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: PH STOMATIN PH1511
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3219
Polymers51,8953
Non-polymers4276
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-22 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.473, 111.473, 91.768
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: 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 PH STOMATIN PH1511 / Uncharacterized protein PH1511


Mass: 1158.473 Da / Num. of mol.: 1 / Fragment: 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, 150 molecules

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


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


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


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


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0M imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2010 / 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: 2.25→20 Å / Num. obs: 27554 / % possible obs: 98.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 67.9
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 9.8 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BPP

3bpp


Resolution: 2.25→19.74 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.102 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 2738 10 %RANDOM
Rwork0.2121 ---
obs0.2157 27366 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.3 Å2 / Biso mean: 52.386 Å2 / Biso min: 11.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 28 144 3607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223520
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9854776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23124.82139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94515602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4711516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212597
X-RAY DIFFRACTIONr_mcbond_it0.5891.52222
X-RAY DIFFRACTIONr_mcangle_it1.15123609
X-RAY DIFFRACTIONr_scbond_it2.01831298
X-RAY DIFFRACTIONr_scangle_it3.3724.51167
LS refinement shellResolution: 2.253→2.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 195 -
Rwork0.253 1810 -
all-2005 -
obs--99.8 %
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)
12.68231.51190.20784.258-0.54812.6177-0.15180.0211-0.1288-0.11450.0323-0.4268-0.2076-0.0520.11960.06050.00810.02320.01470.00670.058625.5744.85819.226
22.934-0.1398-0.46392.95460.64533.5506-0.2636-0.02580.2396-0.45820.13460.05310.01710.07020.1290.1779-0.0242-0.09450.0213-0.01030.107426.04442.53520.732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 237
2X-RAY DIFFRACTION2B19 - 237

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