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- PDB-5yzo: Crystal structure of S9 peptidase mutant (S514A) from Deinococcus... -

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Basic information

Entry
Database: PDB / ID: 5yzo
TitleCrystal structure of S9 peptidase mutant (S514A) 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, 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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,10719
Polymers290,8514
Non-polymers1,25615
Water57,9363216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16240 Å2
ΔGint-26 kcal/mol
Surface area89090 Å2
Unit cell
Length a, b, c (Å)77.195, 190.015, 119.548
Angle α, β, γ (deg.)90.00, 108.46, 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: 72712.797 Da / Num. of mol.: 4 / Mutation: S514A
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q9RXY9
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3216 / 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: 2.86 Å3/Da / Density % sol: 56.98 % / Description: parallelepiped, size 200-300 microns
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.3
Details: 40mM potassium phosphate, 20% PEG 8000, 20% glycerol
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: May 13, 2016 / 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: 1.7→47.9 Å / Num. obs: 356745 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 16.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 2 / Num. unique obs: 17647 / CC1/2: 0.738 / Rpim(I) all: 0.409 / Rrim(I) all: 1.004 / % possible all: 99.9

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Processing

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

5yzn


Resolution: 1.7→37.798 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.98
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 17744 4.98 %Random selection
Rwork0.1683 ---
obs0.1696 356416 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20163 0 72 3216 23451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720908
X-RAY DIFFRACTIONf_angle_d0.89228512
X-RAY DIFFRACTIONf_dihedral_angle_d13.1912130
X-RAY DIFFRACTIONf_chiral_restr0.0562937
X-RAY DIFFRACTIONf_plane_restr0.0073812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.31296020.265711279X-RAY DIFFRACTION100
1.7193-1.73950.31166210.258111254X-RAY DIFFRACTION100
1.7395-1.76080.2785510.242211313X-RAY DIFFRACTION100
1.7608-1.78310.26485900.231911260X-RAY DIFFRACTION100
1.7831-1.80650.26675710.233611289X-RAY DIFFRACTION100
1.8065-1.83130.25845660.220411314X-RAY DIFFRACTION100
1.8313-1.85740.24725830.216511245X-RAY DIFFRACTION100
1.8574-1.88510.25315950.220111349X-RAY DIFFRACTION100
1.8851-1.91460.2466120.2211187X-RAY DIFFRACTION100
1.9146-1.9460.26895970.224311271X-RAY DIFFRACTION100
1.946-1.97950.24745830.21211343X-RAY DIFFRACTION100
1.9795-2.01550.24675740.199111242X-RAY DIFFRACTION100
2.0155-2.05430.23515980.194111271X-RAY DIFFRACTION100
2.0543-2.09620.21635800.190111386X-RAY DIFFRACTION100
2.0962-2.14180.21716210.185411262X-RAY DIFFRACTION100
2.1418-2.19160.19825910.178211186X-RAY DIFFRACTION100
2.1916-2.24640.21216090.181711294X-RAY DIFFRACTION100
2.2464-2.30720.21876040.185411289X-RAY DIFFRACTION100
2.3072-2.3750.21235890.175111246X-RAY DIFFRACTION100
2.375-2.45170.20546160.170811275X-RAY DIFFRACTION100
2.4517-2.53930.20075580.164911307X-RAY DIFFRACTION100
2.5393-2.64090.2116130.168511274X-RAY DIFFRACTION100
2.6409-2.76110.18115770.160811320X-RAY DIFFRACTION100
2.7611-2.90660.18245830.156511303X-RAY DIFFRACTION100
2.9066-3.08860.17655940.150811309X-RAY DIFFRACTION100
3.0886-3.3270.16775870.149911294X-RAY DIFFRACTION100
3.327-3.66150.16755850.144511307X-RAY DIFFRACTION100
3.6615-4.19080.15246190.135511227X-RAY DIFFRACTION100
4.1908-5.27770.13865890.124511375X-RAY DIFFRACTION100
5.2777-37.80760.16425860.155511401X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.1189 Å / Origin y: -46.8818 Å / Origin z: -32.1251 Å
111213212223313233
T0.1602 Å20.005 Å2-0.0126 Å2-0.182 Å2-0.004 Å2--0.1606 Å2
L0.0232 °20.0177 °2-0.0218 °2-0.2267 °2-0.0498 °2--0.0837 °2
S0.0064 Å °-0.0125 Å °0.0057 Å °0.0289 Å °0.0042 Å °0.0275 Å °-0.0077 Å °-0.0034 Å °-0.0115 Å °
Refinement TLS groupSelection details: all

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