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- PDB-6m4b: 1510-N membrane-bound stomatin-specific protease S97A mutant -

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Basic information

Entry
Database: PDB / ID: 6m4b
Title1510-N membrane-bound stomatin-specific protease S97A mutant
ComponentsMembrane-bound protease PH1510
KeywordsHYDROLASE / alpha/beta motif / protease / membrane protein stomatin
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / membrane
Similarity search - Function
Archaeal protein PH0471, N-terminal / : / : / NfeD integral membrane domain / NfeD1b, N-terminal domain / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...Archaeal protein PH0471, N-terminal / : / : / NfeD integral membrane domain / NfeD1b, N-terminal domain / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / 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
Membrane-bound protease PH1510
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsYokoyama, H. / Suzuki, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K07316 Japan
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2020
Title: Inactive dimeric structure of the protease domain of stomatin operon partner protein.
Authors: Yokoyama, H. / Suzuki, K. / Hara, K. / Matsui, I. / Hashimoto, H.
#1: 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.
History
DepositionMar 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-bound protease PH1510
B: Membrane-bound protease PH1510
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0124
Polymers50,8202
Non-polymers1922
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-25 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.731, 124.731, 56.545
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 19 - 225 / Label seq-ID: 5 - 211

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Membrane-bound protease PH1510 / NfeD homolog / Stomatin operon partner protein / STOPP


Mass: 25410.129 Da / Num. of mol.: 2 / Mutation: S97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1510 / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: O59179, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.18 M ammonium sulfate, 27% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 27, 2014 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 24012 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.9
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3490 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3viv

3viv


Resolution: 2.25→19.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.167 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.211
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2411 10.1 %RANDOM
Rwork0.1919 ---
obs0.1961 21579 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.07 Å2 / Biso mean: 52.99 Å2 / Biso min: 28.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 2.25→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 10 53 3239
Biso mean--77.25 49.43 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023240
X-RAY DIFFRACTIONr_bond_other_d0.0060.023176
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9794406
X-RAY DIFFRACTIONr_angle_other_deg1.28937304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.535412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73724.769130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86415552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2771516
X-RAY DIFFRACTIONr_chiral_restr0.0980.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213654
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02686
Refine LS restraints NCS

Ens-ID: 1 / Number: 25924 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 170 -
Rwork0.263 1575 -
all-1745 -
obs--100 %

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