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- PDB-6igp: Crystal structure of S9 peptidase (inactive state)from Deinococcu... -

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Basic information

Entry
Database: PDB / ID: 6igp
TitleCrystal structure of S9 peptidase (inactive state)from Deinococcus radiodurans R1 in P212121
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: 2.4 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 / _citation_author.identifier_ORCID
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)291,2848
Polymers290,9154
Non-polymers3684
Water17,294960
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, molecular weight of the protein corresponds to 265 kDa based on the elution profile obtained by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-34 kcal/mol
Surface area83880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.857, 130.492, 194.973
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.65 Å3/Da / Density % sol: 53.56 % / Description: plate like crystals (~100 microns)
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.31
Details: 50mM Tris-Cl pH 8.5, 200mM ammonium-citrate, 10mM calcium chloride, 14 % PEG 3350
PH range: 5.0-5.5

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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: Sep 29, 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: 2.4→48.74 Å / Num. obs: 119902 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 26.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.052 / Rrim(I) all: 0.165 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 10 % / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 3 / Num. unique obs: 5851 / CC1/2: 0.876 / Rpim(I) all: 0.288 / Rrim(I) all: 0.912 / % 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: 2.4→48.74 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 5987 5 %Random selection
Rwork0.1849 ---
obs0.1866 119705 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17926 0 24 960 18910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618487
X-RAY DIFFRACTIONf_angle_d0.87725230
X-RAY DIFFRACTIONf_dihedral_angle_d3.69810580
X-RAY DIFFRACTIONf_chiral_restr0.0562664
X-RAY DIFFRACTIONf_plane_restr0.0063332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.24751960.22363740X-RAY DIFFRACTION100
2.4273-2.45580.25441860.21823767X-RAY DIFFRACTION100
2.4558-2.48580.23741770.21153762X-RAY DIFFRACTION100
2.4858-2.51720.27352080.21533752X-RAY DIFFRACTION100
2.5172-2.55040.2652000.21023772X-RAY DIFFRACTION100
2.5504-2.58530.27592050.21523701X-RAY DIFFRACTION100
2.5853-2.62220.25591930.20933767X-RAY DIFFRACTION100
2.6222-2.66140.26771980.21143801X-RAY DIFFRACTION100
2.6614-2.7030.26391700.21253748X-RAY DIFFRACTION100
2.703-2.74730.26721930.20843760X-RAY DIFFRACTION100
2.7473-2.79460.25471900.2163786X-RAY DIFFRACTION100
2.7946-2.84540.24631680.21873780X-RAY DIFFRACTION100
2.8454-2.90020.25881910.2163806X-RAY DIFFRACTION100
2.9002-2.95940.27632010.2033752X-RAY DIFFRACTION100
2.9594-3.02370.24941850.19893785X-RAY DIFFRACTION100
3.0237-3.0940.23541900.18943784X-RAY DIFFRACTION100
3.094-3.17140.22982030.193785X-RAY DIFFRACTION100
3.1714-3.25710.21131930.18923781X-RAY DIFFRACTION100
3.2571-3.35290.22242140.19263769X-RAY DIFFRACTION100
3.3529-3.46110.1951700.19443812X-RAY DIFFRACTION100
3.4611-3.58480.23372060.18973767X-RAY DIFFRACTION100
3.5848-3.72830.17662150.17363800X-RAY DIFFRACTION100
3.7283-3.89790.20642180.16823778X-RAY DIFFRACTION100
3.8979-4.10330.19572180.1623789X-RAY DIFFRACTION100
4.1033-4.36020.19752260.14893798X-RAY DIFFRACTION100
4.3602-4.69660.16342360.1423793X-RAY DIFFRACTION100
4.6966-5.16880.17562250.14233825X-RAY DIFFRACTION100
5.1688-5.91560.18112110.16253857X-RAY DIFFRACTION100
5.9156-7.44880.19891870.19283922X-RAY DIFFRACTION100
7.4488-48.75330.20782140.18913979X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3619-0.05030.15330.6445-0.11960.38880.00730.0506-0.0977-0.06860.01010.0121-0.0298-0.0381-0.01820.1690.01180.00860.141-0.00560.11877.4065-24.8558-8.9453
21.26010.1502-0.12140.5447-0.01730.3065-0.0204-0.1918-0.12280.1294-0.00220.0395-0.01280.0210.01530.18870.0097-0.0050.17540.02850.146826.5763-25.813-88.409
30.76750.10710.06950.4103-0.04731.3223-0.0211-0.1426-0.03530.143-0.05430.0670.1226-0.0710.0820.2186-0.01410.01130.1564-0.01940.2636-19.2117-18.7866-67.0637
40.9992-0.2982-0.07190.6449-0.02281.12450.14950.43810.1474-0.2369-0.1611-0.11280.11040.03940.01820.25950.07650.0320.37470.10420.196953.5417-18.8175-29.9233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 9:655)
2X-RAY DIFFRACTION2(chain B and resseq 7:655)
3X-RAY DIFFRACTION3(chain C and resseq 7:655)
4X-RAY DIFFRACTION4(chain D and resseq 7:655)

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