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- PDB-5yzm: Crystal structure of S9 peptidase (inactive form) from Deinococcu... -

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Basic information

Entry
Database: PDB / ID: 5yzm
TitleCrystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1
ComponentsAcyl-peptide hydrolase, putative
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
Similarity search - Domain/homology
ACETATE ION / Acyl-peptide hydrolase, putative
Similarity search - Component
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,1518
Polymers290,9154
Non-polymers2364
Water18,9521052
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-34 kcal/mol
Surface area85050 Å2
Unit cell
Length a, b, c (Å)73.702, 195.092, 107.715
Angle α, β, γ (deg.)90.00, 99.97, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q9RXY9
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1052 / 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: 53.08 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.47
Details: 50mM sodium acetate, pH 4.5, 200mM sodium chloride, 10mM magnesium chloride, 12% PEG 3350
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: Apr 10, 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→48.77 Å / Num. obs: 132199 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6511 / CC1/2: 0.719 / Rpim(I) all: 0.38 / Rrim(I) all: 0.742 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
REFMACrefinement
Cootmodel building
RESOLVEmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HXE

4hxe


Resolution: 2.3→46.867 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3
RfactorNum. reflection% reflection
Rfree0.2193 6534 4.95 %
Rwork0.1894 --
obs0.1909 132060 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18355 0 16 1052 19423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218928
X-RAY DIFFRACTIONf_angle_d0.57825827
X-RAY DIFFRACTIONf_dihedral_angle_d11.89810873
X-RAY DIFFRACTIONf_chiral_restr0.0432713
X-RAY DIFFRACTIONf_plane_restr0.0043432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.28492160.26054137X-RAY DIFFRACTION100
2.3261-2.35350.31092260.26244171X-RAY DIFFRACTION100
2.3535-2.38220.3132030.25354259X-RAY DIFFRACTION100
2.3822-2.41240.28872300.24484092X-RAY DIFFRACTION100
2.4124-2.44410.27252040.2344240X-RAY DIFFRACTION100
2.4441-2.47760.26672120.23484163X-RAY DIFFRACTION100
2.4776-2.5130.29462300.23834198X-RAY DIFFRACTION100
2.513-2.55050.25642190.23124177X-RAY DIFFRACTION100
2.5505-2.59030.24912000.22784181X-RAY DIFFRACTION100
2.5903-2.63280.26852290.22534226X-RAY DIFFRACTION100
2.6328-2.67820.27822050.22684116X-RAY DIFFRACTION100
2.6782-2.72690.26812140.22424229X-RAY DIFFRACTION100
2.7269-2.77930.24962360.21944187X-RAY DIFFRACTION100
2.7793-2.8360.27162010.22944206X-RAY DIFFRACTION100
2.836-2.89770.26712180.21944159X-RAY DIFFRACTION100
2.8977-2.96510.25512280.21214165X-RAY DIFFRACTION100
2.9651-3.03920.24431840.21294212X-RAY DIFFRACTION100
3.0392-3.12140.26782410.20994184X-RAY DIFFRACTION100
3.1214-3.21320.26332330.21034201X-RAY DIFFRACTION100
3.2132-3.31690.2312110.20664176X-RAY DIFFRACTION100
3.3169-3.43540.22722280.19614146X-RAY DIFFRACTION100
3.4354-3.57290.22882150.19114176X-RAY DIFFRACTION99
3.5729-3.73550.20492080.17544205X-RAY DIFFRACTION99
3.7355-3.93230.19662410.17464131X-RAY DIFFRACTION99
3.9323-4.17860.19112210.15954184X-RAY DIFFRACTION100
4.1786-4.50090.15982200.14434185X-RAY DIFFRACTION100
4.5009-4.95340.14742160.13534203X-RAY DIFFRACTION100
4.9534-5.66920.16652100.14694243X-RAY DIFFRACTION100
5.6692-7.13850.20332270.17074180X-RAY DIFFRACTION100
7.1385-46.87640.17082080.16444194X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -4.6556 Å / Origin y: -27.159 Å / Origin z: -31.2665 Å
111213212223313233
T0.2591 Å2-0.0096 Å20.0049 Å2-0.3302 Å20.0043 Å2--0.2789 Å2
L-0.0447 °20.0562 °20.007 °2-0.2978 °20.0847 °2---0.0206 °2
S-0.0083 Å °-0.0188 Å °-0.0085 Å °-0.0025 Å °0.0323 Å °0.0236 Å °-0.012 Å °-0.0215 Å °-0.0248 Å °
Refinement TLS groupSelection details: all

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