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- PDB-6ikg: Crystal structure of substrate-bound S9 peptidase (S514A mutant) ... -

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Basic information

Entry
Database: PDB / ID: 6ikg
TitleCrystal structure of substrate-bound S9 peptidase (S514A mutant) from Deinococcus radiodurans
Components
  • Acyl-peptide hydrolase, putative
  • MET-ALA-ALA
KeywordsHYDROLASE / Serine peptidase / Merops S9 / POP family
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
WD40-like beta propeller / WD40-like Beta Propeller Repeat / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acyl-peptide hydrolase, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Deinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYadav, P. / Kumar, A. / Goyal, V.D. / Makde, R.D.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms.
Authors: Yadav, P. / Goyal, V.D. / Gaur, N.K. / Kumar, A. / Gokhale, S.M. / Jamdar, S.N. / Makde, R.D.
History
DepositionOct 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 20, 2019Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.title
Revision 1.4Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-peptide hydrolase, putative
B: Acyl-peptide hydrolase, putative
C: Acyl-peptide hydrolase, putative
D: Acyl-peptide hydrolase, putative
E: MET-ALA-ALA
F: MET-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,80210
Polymers291,4346
Non-polymers3684
Water13,655758
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15050 Å2
ΔGint-57 kcal/mol
Surface area87660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.649, 214.636, 92.022
Angle α, β, γ (deg.)90.00, 102.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl-peptide hydrolase, putative


Mass: 72712.797 Da / Num. of mol.: 4 / Fragment: UNP residues 2-655 / Mutation: S514A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Gene: DR_0165 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RXY9
#2: Protein/peptide MET-ALA-ALA


Mass: 291.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Deinococcus radiodurans (radioresistant)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / 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: 2.37 Å3/Da / Density % sol: 48 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.4 / Details: 40mM potassium phosphate 30 PEG8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2018 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→46.98 Å / Num. obs: 119554 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.065 / Rrim(I) all: 0.142 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 2 / Num. unique obs: 5872 / CC1/2: 0.655 / Rpim(I) all: 0.504 / Rrim(I) all: 1.094 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YZO

5yzo


Resolution: 2.3→46.978 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.72
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 5981 5.01 %Random selection
Rwork0.2074 ---
obs0.2088 119478 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19790 0 24 758 20572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320412
X-RAY DIFFRACTIONf_angle_d0.64527889
X-RAY DIFFRACTIONf_dihedral_angle_d3.93911764
X-RAY DIFFRACTIONf_chiral_restr0.0472920
X-RAY DIFFRACTIONf_plane_restr0.0043723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.3082100.29713697X-RAY DIFFRACTION100
2.3261-2.35350.32262070.28473799X-RAY DIFFRACTION100
2.3535-2.38220.32772140.28133793X-RAY DIFFRACTION100
2.3822-2.41240.30141860.26623755X-RAY DIFFRACTION100
2.4124-2.44410.28221890.26133763X-RAY DIFFRACTION100
2.4441-2.47760.281890.24753845X-RAY DIFFRACTION100
2.4776-2.5130.30211710.25363754X-RAY DIFFRACTION100
2.513-2.55050.29491800.25633841X-RAY DIFFRACTION100
2.5505-2.59030.29451980.24923732X-RAY DIFFRACTION100
2.5903-2.63280.32172110.25713829X-RAY DIFFRACTION100
2.6328-2.67820.2531680.25053778X-RAY DIFFRACTION100
2.6782-2.72690.27842170.23513741X-RAY DIFFRACTION100
2.7269-2.77930.24661940.23353824X-RAY DIFFRACTION100
2.7793-2.8360.26341730.23253785X-RAY DIFFRACTION100
2.836-2.89770.26792080.23423778X-RAY DIFFRACTION100
2.8977-2.96510.2691870.22953823X-RAY DIFFRACTION100
2.9651-3.03920.24551870.22043771X-RAY DIFFRACTION100
3.0392-3.12140.25442080.21553792X-RAY DIFFRACTION100
3.1214-3.21320.23622090.2163748X-RAY DIFFRACTION100
3.2132-3.31690.22482190.20953761X-RAY DIFFRACTION100
3.3169-3.43540.23242100.20283794X-RAY DIFFRACTION100
3.4354-3.57290.21711920.20563815X-RAY DIFFRACTION100
3.5729-3.73550.2011830.1943763X-RAY DIFFRACTION100
3.7355-3.93230.22612070.18593777X-RAY DIFFRACTION100
3.9323-4.17860.20162160.17313814X-RAY DIFFRACTION100
4.1786-4.5010.15991860.15843793X-RAY DIFFRACTION100
4.501-4.95350.18962420.16233754X-RAY DIFFRACTION100
4.9535-5.66920.21591960.1733799X-RAY DIFFRACTION100
5.6692-7.13860.21452060.19483829X-RAY DIFFRACTION100
7.1386-46.98740.21112180.17443750X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 50.9239 Å / Origin y: 44.2586 Å / Origin z: 120.163 Å
111213212223313233
T0.0971 Å2-0.0089 Å20.0154 Å2-0.1278 Å2-0.0023 Å2--0.1117 Å2
L0.0292 °20.0118 °20.0084 °2-0.2263 °20.0354 °2--0.0159 °2
S-0.0045 Å °0.0029 Å °0.0206 Å °0.0051 Å °-0.0104 Å °0.0629 Å °-0.0236 Å °0.0137 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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