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- PDB-7ep9: The structure of carboxypeptidase from Fusobacterium nucleatum -

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Basic information

Entry
Database: PDB / ID: 7ep9
TitleThe structure of carboxypeptidase from Fusobacterium nucleatum
ComponentsS9 family peptidase
KeywordsHYDROLASE / Fusobacterium nucleatum / serine peptidase / crystal screening
Function / homologyPeptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / serine-type peptidase activity / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S9 family peptidase
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å
AuthorsWang, X. / Jiang, Y.L.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural and biochemical analyses of the tetrameric carboxypeptidase S9Cfn from Fusobacterium nucleatum.
Authors: Wang, X. / Cheng, M.T. / Chen, Z.P. / Jiang, Y.L. / Ge, Y.S. / Xia, R. / Hou, W.T.
History
DepositionApr 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: S9 family peptidase
A: S9 family peptidase
B: S9 family peptidase
C: S9 family peptidase


Theoretical massNumber of molelcules
Total (without water)306,5034
Polymers306,5034
Non-polymers00
Water8,827490
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-53 kcal/mol
Surface area96050 Å2
Unit cell
Length a, b, c (Å)192.004, 124.797, 128.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
S9 family peptidase


Mass: 76625.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: BKN39_05345 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S1MBE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 21%PEG_2000 and 0.1 M Tris pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 95180 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.84 / Net I/σ(I): 10.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.7 / Num. unique obs: 94966

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
PDB_EXTRACT3.27data extraction
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.604→44.83 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 4942 5.2 %
Rwork0.2294 90024 -
obs0.2317 94966 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.19 Å2 / Biso mean: 38.4944 Å2 / Biso min: 11.67 Å2
Refinement stepCycle: final / Resolution: 2.604→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21636 0 0 490 22126
Biso mean---33.68 -
Num. residues----2640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.604-2.63330.36621430.3137283195
2.6333-2.66430.37371650.29672939100
2.6643-2.69680.36671580.28432993100
2.6968-2.73090.32211440.29882994100
2.7309-2.76690.34011660.28073002100
2.7669-2.80480.36061680.28482957100
2.8048-2.84480.35111700.29392974100
2.8448-2.88730.32821720.29132969100
2.8873-2.93240.36841820.27832964100
2.9324-2.98050.28771740.26292959100
2.9805-3.03180.33081630.26082996100
3.0318-3.0870.33421450.26643005100
3.087-3.14630.32121290.25943026100
3.1463-3.21050.29731640.26143003100
3.2105-3.28030.33131670.25262988100
3.2803-3.35660.31971620.25082981100
3.3566-3.44050.2721550.24683007100
3.4405-3.53350.30431660.23453005100
3.5335-3.63740.3181760.23562977100
3.6374-3.75480.29561640.22593026100
3.7548-3.88890.27211480.22233030100
3.8889-4.04450.26281590.21973014100
4.0445-4.22850.23381640.20543006100
4.2285-4.45120.23421830.1953038100
4.4512-4.72980.23941730.19413009100
4.7298-5.09450.2321860.18263021100
5.0945-5.60630.22341830.18673057100
5.6063-6.41560.20011620.19623089100
6.4156-8.07520.21481790.2013082100
8.0752-44.830.19171720.1862308295

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