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- PDB-6nag: X-ray structure of a secreted C11 cysteine protease from Bacteroi... -

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Basic information

Entry
Database: PDB / ID: 6nag
TitleX-ray structure of a secreted C11 cysteine protease from Bacteroides thetaiotaomicron "iotapain
ComponentsClostripain-related protein
KeywordsHYDROLASE / C11 protease / secreted / microbiome / commensal
Function / homologyPeptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / PROLINE / Clostripain-related protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.683 Å
AuthorsWolan, D.W. / Gonzalez-Paez, G.E. / Roncase, E.J.
CitationJournal: Biochemistry / Year: 2019
Title: X-ray Structures of Two Bacteroides thetaiotaomicron C11 Proteases in Complex with Peptide-Based Inhibitors.
Authors: Roncase, E.J. / Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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: Clostripain-related protein
B: Clostripain-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9545
Polymers82,6092
Non-polymers3453
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-2 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.677, 157.677, 119.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Clostripain-related protein


Mass: 41304.375 Da / Num. of mol.: 2 / Mutation: R154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0727 / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q8A9T8
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO2 / Details: Additive
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 4.8 Å3/Da / Density % sol: 74.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Na Citrate, pH 5.0, 50% MPD, 10 mM L-Proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2017 / Details: Rh coated
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.68→45.52 Å / Num. obs: 47832 / % possible obs: 98.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.081 / Rrim(I) all: 0.178 / Net I/σ(I): 11.2
Reflection shellResolution: 2.68→2.73 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2368 / CC1/2: 0.719 / Rpim(I) all: 0.339 / Rrim(I) all: 0.735 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L20

5l20


Resolution: 2.683→45.517 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 1084 2.27 %
Rwork0.1762 --
obs0.177 47802 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.683→45.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5550 0 24 609 6183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025730
X-RAY DIFFRACTIONf_angle_d0.5327790
X-RAY DIFFRACTIONf_dihedral_angle_d10.5022039
X-RAY DIFFRACTIONf_chiral_restr0.021870
X-RAY DIFFRACTIONf_plane_restr0.002981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6827-2.80480.30241300.24795712X-RAY DIFFRACTION98
2.8048-2.95270.26931340.23135849X-RAY DIFFRACTION99
2.9527-3.13760.24981390.21355828X-RAY DIFFRACTION100
3.1376-3.37980.22071360.18595811X-RAY DIFFRACTION100
3.3798-3.71980.19591340.1685772X-RAY DIFFRACTION98
3.7198-4.25770.18921370.14435894X-RAY DIFFRACTION100
4.2577-5.36290.15571360.14095854X-RAY DIFFRACTION98
5.3629-45.5240.21011380.17095998X-RAY DIFFRACTION98

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