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- PDB-6f9m: The LIPY/F-motif in an intracellular subtilisin protease is invol... -

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Basic information

Entry
Database: PDB / ID: 6f9m
TitleThe LIPY/F-motif in an intracellular subtilisin protease is involved in inhibition
ComponentsSerine protease
KeywordsHYDROLASE / ISP / LIPY/F-motif / subtilisin / protease structure
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Serine protease
Similarity search - Component
Biological speciesPlanococcus plakortidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.298 Å
AuthorsBjerga, G.E.K. / Larsen, O. / Arsin, H. / Williamson, A.K. / Garcia-Moyano, A. / Leiros, I. / Puntervoll, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway221568 Norway
CitationJournal: Proteins / Year: 2018
Title: Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition.
Authors: Bjerga, G.E.K. / Larsen, O. / Williamson, A. / Garcia-Moyano, A. / Leiros, I. / Puntervoll, P.
History
DepositionDec 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease
B: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6148
Polymers71,1492
Non-polymers4646
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-16 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.170, 85.180, 104.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine protease


Mass: 35574.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planococcus plakortidis (bacteria) / Gene: BBI15_13285 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A3B6UEW8*PLUS
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.25 M NH4Ac, 21.73 % PEG 1500, 0.1 M Na-Citrate pH 4.0
Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.298→66.05 Å / Num. obs: 142753 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 17.39 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 16.4
Reflection shellResolution: 1.298→1.32 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7606 / Rpim(I) all: 0.412 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XRM

2xrm


Resolution: 1.298→44.563 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.04
RfactorNum. reflection% reflection
Rfree0.1503 1992 1.4 %
Rwork0.1302 --
obs0.1304 142740 92.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.92 Å2 / Biso mean: 24.6485 Å2 / Biso min: 11.81 Å2
Refinement stepCycle: final / Resolution: 1.298→44.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 64 549 5045
Biso mean--31.63 37.2 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074670
X-RAY DIFFRACTIONf_angle_d0.9626361
X-RAY DIFFRACTIONf_chiral_restr0.08711
X-RAY DIFFRACTIONf_plane_restr0.007854
X-RAY DIFFRACTIONf_dihedral_angle_d14.3861701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2977-1.33020.24991730.22941069510868100
1.3302-1.36620.20791700.1991075610926100
1.3662-1.40640.20151420.1761078410926100
1.4064-1.45180.20961370.15621083510972100
1.4518-1.50370.18741210.13441079110912100
1.5037-1.56390.14241590.11691081510974100
1.5639-1.6350.14441600.1071084011000100
1.635-1.72120.14621410.101299881012999
1.7212-1.82910.13541690.098102741044399
1.8291-1.97030.1423990.10367333743267
1.9703-2.16860.15911050.10836957706264
2.1686-2.48240.10611400.113104481058895
2.4824-3.12740.14321350.13259727986288
3.1274-44.58950.15991410.1437105051064692

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