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- PDB-6igq: Crystal structure of inactive state of S9 peptidase from Deinococ... -

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Basic information

Entry
Database: PDB / ID: 6igq
TitleCrystal structure of inactive state of S9 peptidase from Deinococcus radiodurans R1 (PMSF treated)
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 str. R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYadav, P. / Goyal, V.D. / Kumar, A. / 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
DepositionSep 25, 2018Deposition 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,31219
Polymers290,9154
Non-polymers1,39715
Water17,871992
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, molecular weight of protein corresponds to 265 kDa based on the elution profile obtained by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-113 kcal/mol
Surface area82820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.658, 129.989, 194.130
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


Mass: 72728.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans str. R1 (radioresistant)
Strain: R1 / Gene: DR_0165 / Plasmid: pST50Tr / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): plysS / References: UniProt: Q9RXY9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / 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: 2.62 Å3/Da / Density % sol: 53.1 % / Description: cubiod crystals (150-200 micron)
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.31
Details: 0.17M ammonium sulphate, 25.5% PEG 4000, 15% glycerol
PH range: 4.8-5.3

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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: Oct 30, 2015 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.3→39.89 Å / Num. obs: 134697 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.062 / Rrim(I) all: 0.169 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6616 / CC1/2: 0.781 / Rpim(I) all: 0.391 / Rrim(I) all: 1.072 / % possible all: 100

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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: 5YZM

5yzm


Resolution: 2.3→39.872 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 6737 5.01 %Random selection
Rwork0.1918 ---
obs0.1935 134499 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18146 0 86 992 19224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618795
X-RAY DIFFRACTIONf_angle_d0.8125645
X-RAY DIFFRACTIONf_dihedral_angle_d3.69212788
X-RAY DIFFRACTIONf_chiral_restr0.0512695
X-RAY DIFFRACTIONf_plane_restr0.0063389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.27632470.25494211X-RAY DIFFRACTION100
2.3261-2.35350.30092350.24914202X-RAY DIFFRACTION100
2.3535-2.38220.29022080.24544205X-RAY DIFFRACTION100
2.3822-2.41230.27682030.24344220X-RAY DIFFRACTION100
2.4123-2.44410.26542160.23434262X-RAY DIFFRACTION100
2.4441-2.47760.24942070.22734232X-RAY DIFFRACTION100
2.4776-2.5130.25562260.22824201X-RAY DIFFRACTION100
2.513-2.55050.29082360.22524254X-RAY DIFFRACTION100
2.5505-2.59030.26862240.22484192X-RAY DIFFRACTION100
2.5903-2.63280.26122170.22144216X-RAY DIFFRACTION100
2.6328-2.67810.25441990.22544263X-RAY DIFFRACTION100
2.6781-2.72680.25672150.21994261X-RAY DIFFRACTION100
2.7268-2.77930.25652170.20984221X-RAY DIFFRACTION100
2.7793-2.8360.2511820.21774276X-RAY DIFFRACTION100
2.836-2.89760.22112200.20614257X-RAY DIFFRACTION100
2.8976-2.9650.2672220.20224223X-RAY DIFFRACTION100
2.965-3.03910.22622060.20314257X-RAY DIFFRACTION100
3.0391-3.12130.24612170.19854252X-RAY DIFFRACTION100
3.1213-3.21310.25392290.19954251X-RAY DIFFRACTION100
3.2131-3.31680.23642330.20494243X-RAY DIFFRACTION100
3.3168-3.43520.22612060.19714269X-RAY DIFFRACTION100
3.4352-3.57270.23182230.18784263X-RAY DIFFRACTION100
3.5727-3.73520.19352460.17494272X-RAY DIFFRACTION100
3.7352-3.93190.19512350.17864264X-RAY DIFFRACTION100
3.9319-4.1780.20232650.1644242X-RAY DIFFRACTION100
4.178-4.50020.17432440.14884277X-RAY DIFFRACTION100
4.5002-4.95240.18082720.14784277X-RAY DIFFRACTION100
4.9524-5.66720.18782320.1544346X-RAY DIFFRACTION100
5.6672-7.13340.2152230.18334373X-RAY DIFFRACTION100
7.1334-39.87820.19452320.17244480X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -16.7989 Å / Origin y: -22.0786 Å / Origin z: 48.3392 Å
111213212223313233
T0.222 Å2-0.008 Å20.003 Å2-0.1981 Å2-0.0248 Å2--0.2607 Å2
L-0.028 °2-0.016 °20.0483 °2--0.0243 °20.0061 °2--0.1716 °2
S-0.0225 Å °-0.0022 Å °-0.0173 Å °-0.0025 Å °-0.0126 Å °-0.0024 Å °0.0222 Å °-0.0393 Å °0.0353 Å °
Refinement TLS groupSelection details: all

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