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- PDB-8wt1: Crystal structure of S9 carboxypeptidase from Geobacillus steroth... -

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Basic information

Entry
Database: PDB / ID: 8wt1
TitleCrystal structure of S9 carboxypeptidase from Geobacillus sterothermophilus
ComponentsS9 family peptidase
KeywordsHYDROLASE / Carboxypeptidase / Prolyl oligopeptidase / Oligomerization / Acylaminoacyl.
Function / homology
Function and homology information


serine-type peptidase 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
ALANINE / CITRATE ANION / S9 family peptidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus ATCC 12980 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChandravanshi, K. / Kumar, A. / Sen, C. / Singh, R. / Bhange, G.B. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)IF190153 India
CitationJournal: Febs Lett. / Year: 2024
Title: Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity.
Authors: Chandravanshi, K. / Singh, R. / Bhange, G.N. / Kumar, A. / Yadav, P. / Kumar, A. / Makde, R.D.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S9 family peptidase
B: S9 family peptidase
C: S9 family peptidase
D: S9 family peptidase
E: S9 family peptidase
F: S9 family peptidase
G: S9 family peptidase
H: S9 family peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)627,526121
Polymers617,6588
Non-polymers9,867113
Water37,4892081
1
A: S9 family peptidase
B: S9 family peptidase
C: S9 family peptidase
H: S9 family peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,17366
Polymers308,8294
Non-polymers5,34462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: S9 family peptidase
E: S9 family peptidase
F: S9 family peptidase
G: S9 family peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,35355
Polymers308,8294
Non-polymers4,52351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.123, 75.443, 219.740
Angle α, β, γ (deg.)90.000, 93.270, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
S9 family peptidase


Mass: 77207.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: UPI0006AC02FD, WP_053532245
Source: (gene. exp.) Geobacillus stearothermophilus ATCC 12980 (bacteria)
Gene: D9548_14720 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3L7D5Q2

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Non-polymers , 6 types, 2194 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2081 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 294.15 K / Method: microbatch / pH: 4
Details: 0.8 M Ammonium sulphate, 0.1 M sodium citrate pH-4.0, 20 mM MES, 100 mM NaCl (Mixed in 1:1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 2, 2022
RadiationMonochromator: Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→48.94 Å / Num. obs: 394267 / % possible obs: 92.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.064 / Rrim(I) all: 0.125 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 1 / Num. unique obs: 20613 / CC1/2: 0.527 / Rpim(I) all: 0.74 / Rrim(I) all: 1.424 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.94 Å / SU ML: 0.2946 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1511
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2559 19814 5.04 %
Rwork0.212 373435 -
obs0.2142 393249 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.56 Å2
Refinement stepCycle: LAST / Resolution: 2→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40145 0 557 2081 42783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007641656
X-RAY DIFFRACTIONf_angle_d0.875356632
X-RAY DIFFRACTIONf_chiral_restr0.05546084
X-RAY DIFFRACTIONf_plane_restr0.00827274
X-RAY DIFFRACTIONf_dihedral_angle_d8.27775719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.37726910.339913019X-RAY DIFFRACTION96.57
2.02-2.050.3647090.319213253X-RAY DIFFRACTION98.05
2.05-2.070.36727390.314213138X-RAY DIFFRACTION97.99
2.07-2.10.33426920.302513325X-RAY DIFFRACTION98.09
2.1-2.130.35537130.296813139X-RAY DIFFRACTION98.12
2.13-2.150.33546960.284513346X-RAY DIFFRACTION98.13
2.15-2.190.33916810.276213168X-RAY DIFFRACTION98.03
2.19-2.220.33327300.274513369X-RAY DIFFRACTION97.99
2.22-2.220.3213410.32837X-RAY DIFFRACTION57.69
2.28-2.290.31121550.29293369X-RAY DIFFRACTION86.35
2.29-2.330.33766600.258713212X-RAY DIFFRACTION98.14
2.33-2.370.31037330.243813396X-RAY DIFFRACTION98.51
2.37-2.420.29866410.243413317X-RAY DIFFRACTION98.43
2.42-2.470.29166830.233113340X-RAY DIFFRACTION98.4
2.47-2.520.28687310.235913368X-RAY DIFFRACTION98.49
2.52-2.580.28846910.23913270X-RAY DIFFRACTION98.55
2.58-2.640.29157380.233113351X-RAY DIFFRACTION98.59
2.64-2.710.27976890.23813424X-RAY DIFFRACTION98.79
2.71-2.790.27917580.230813384X-RAY DIFFRACTION98.83
2.79-2.880.29417280.229113284X-RAY DIFFRACTION98.54
2.88-2.990.28136830.226613430X-RAY DIFFRACTION98.58
2.99-3.110.26457030.224313415X-RAY DIFFRACTION98.6
3.11-3.250.25846840.217413351X-RAY DIFFRACTION98.28
3.25-3.420.24937260.213513348X-RAY DIFFRACTION97.96
3.42-3.630.24976510.206613259X-RAY DIFFRACTION97.35
3.63-3.910.2315260.18279772X-RAY DIFFRACTION71.54
3.91-4.310.19347740.162513098X-RAY DIFFRACTION96.37
4.31-4.930.19067110.145713163X-RAY DIFFRACTION96.05
4.93-6.210.2057350.166413565X-RAY DIFFRACTION98.39
6.21-48.940.21417220.187113725X-RAY DIFFRACTION97.19

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