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- PDB-5yzn: Crystal structure of S9 peptidase (active form) from Deinococcus ... -

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Basic information

Entry
Database: PDB / ID: 5yzn
TitleCrystal structure of S9 peptidase (active form) from Deinococcus radiodurans R1
ComponentsAcyl-peptide hydrolase, putative
KeywordsHYDROLASE / Serine peptidase / Merops S9 / POP family
Function / homologyWD40-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 / serine-type endopeptidase activity / proteolysis / Acyl-peptide hydrolase, putative
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYadav, P. / Jamdar, S.N. / Kumar, A. / Ghosh, B. / 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
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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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


Theoretical massNumber of molelcules
Total (without water)290,9154
Polymers290,9154
Non-polymers00
Water23,9781331
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-47 kcal/mol
Surface area89460 Å2
Unit cell
Length a, b, c (Å)120.432, 148.223, 190.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acyl-peptide hydrolase, putative / S9 prolyl oligopeptidase


Mass: 72728.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0165 / Plasmid: pST50Tr / Details (production host): pET based plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q9RXY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1331 / 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: 2.92 Å3/Da / Density % sol: 57.85 % / Description: parallelepiped, size 200-300 micron
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.3
Details: 40mM potassium phosphate, 20% glycerol, 16% PEG 8000
PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2015 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.3→39.28 Å / Num. obs: 151191 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.05 / Rrim(I) all: 0.133 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7386 / CC1/2: 0.913 / Rpim(I) all: 0.373 / Rrim(I) all: 1.002 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
REFMACrefinement
Cootmodel building
RESOLVEmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YZM

5yzm


Resolution: 2.3→39.279 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.68
RfactorNum. reflection% reflection
Rfree0.2311 7497 4.99 %
Rwork0.2045 --
obs0.2058 150388 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20100 0 0 1331 21431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220716
X-RAY DIFFRACTIONf_angle_d0.63828293
X-RAY DIFFRACTIONf_dihedral_angle_d13.40411975
X-RAY DIFFRACTIONf_chiral_restr0.0442936
X-RAY DIFFRACTIONf_plane_restr0.0043793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.33442210.30694736X-RAY DIFFRACTION100
2.3261-2.35350.31762360.29544738X-RAY DIFFRACTION100
2.3535-2.38220.33472650.28024690X-RAY DIFFRACTION99
2.3822-2.41230.31532520.28114727X-RAY DIFFRACTION100
2.4123-2.44410.33052380.25974718X-RAY DIFFRACTION100
2.4441-2.47760.28742430.25634743X-RAY DIFFRACTION100
2.4776-2.51290.32082380.26214762X-RAY DIFFRACTION100
2.5129-2.55050.28882290.2574719X-RAY DIFFRACTION100
2.5505-2.59030.27842250.25344763X-RAY DIFFRACTION100
2.5903-2.63280.2712430.24684711X-RAY DIFFRACTION100
2.6328-2.67810.29862560.24464761X-RAY DIFFRACTION100
2.6781-2.72680.28552580.24274736X-RAY DIFFRACTION100
2.7268-2.77930.26822320.23084756X-RAY DIFFRACTION100
2.7793-2.8360.27462710.24444727X-RAY DIFFRACTION100
2.836-2.89760.25592470.23924763X-RAY DIFFRACTION100
2.8976-2.9650.30272650.24574736X-RAY DIFFRACTION100
2.965-3.03910.30822770.23964717X-RAY DIFFRACTION100
3.0391-3.12130.26232610.2324727X-RAY DIFFRACTION100
3.1213-3.21310.25912320.22464780X-RAY DIFFRACTION100
3.2131-3.31670.23782590.21784741X-RAY DIFFRACTION100
3.3167-3.43520.22432460.21474781X-RAY DIFFRACTION100
3.4352-3.57270.21972500.20814763X-RAY DIFFRACTION100
3.5727-3.73510.23512760.1944766X-RAY DIFFRACTION100
3.7351-3.93190.18812380.18164766X-RAY DIFFRACTION99
3.9319-4.1780.18982490.16884765X-RAY DIFFRACTION99
4.178-4.50010.17112460.15014809X-RAY DIFFRACTION99
4.5001-4.95220.15422390.14014825X-RAY DIFFRACTION99
4.9522-5.6670.16142600.15244854X-RAY DIFFRACTION100
5.667-7.13280.20052720.17394904X-RAY DIFFRACTION100
7.1328-39.28450.16622730.15434907X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 132.5933 Å / Origin y: 173.8118 Å / Origin z: 47.5903 Å
111213212223313233
T0.2234 Å2-0.0174 Å20.0024 Å2-0.2136 Å20.0295 Å2--0.2309 Å2
L0.0528 °2-0.0304 °2-0.0451 °2-0.0087 °20.0159 °2--0.1679 °2
S-0.0066 Å °0.0212 Å °0.007 Å °-0.0032 Å °0.0066 Å °0.0235 Å °-0.0151 Å °-0.0554 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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