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- PDB-5l20: Crystal Structure of a Clostripain (BT_0727) from Bacteroides the... -

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Basic information

Entry
Database: PDB / ID: 5l20
TitleCrystal Structure of a Clostripain (BT_0727) from Bacteroides thetaiotaomicron ATCC 29148 in Complex with Peptide Inhibitor BTN-VLTK-AOMK
Components
  • (Clostripain-related protein) x 2
  • Peptide Inhibitor BTN-VLTK-AOMK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Clostripain / peptidase / microbiome / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyPeptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Peptide Inhibitor BTN-VLTK-AOMK / Clostripain-related protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsWolan, D.W. / Roncase, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3U54GM094586-03S1 United States
CitationJournal: To be published
Title: Crystal Structure of a Clostripain (BT_0727) from Bacteroides thetaiotaomicron ATCC 29148 in Complex with Peptide Inhibitor BTN-VLTK-AOMK
Authors: Wolan, D.W. / Roncase, E.J.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clostripain-related protein
B: Clostripain-related protein
C: Peptide Inhibitor BTN-VLTK-AOMK


Theoretical massNumber of molelcules
Total (without water)43,1073
Polymers43,1073
Non-polymers00
Water7,945441
1
A: Clostripain-related protein
C: Peptide Inhibitor BTN-VLTK-AOMK


Theoretical massNumber of molelcules
Total (without water)17,1402
Polymers17,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Clostripain-related protein


Theoretical massNumber of molelcules
Total (without water)25,9671
Polymers25,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.207, 102.885, 84.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-745-

HOH

21B-781-

HOH

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Components

#1: Protein Clostripain-related protein


Mass: 16455.676 Da / Num. of mol.: 1
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 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8A9T8
#2: Protein Clostripain-related protein


Mass: 25966.994 Da / Num. of mol.: 1
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 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8A9T8
#3: Protein/peptide Peptide Inhibitor BTN-VLTK-AOMK


Type: Peptide-like / Class: Inhibitor / Mass: 683.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Peptide Inhibitor BTN-VLTK-AOMK
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsthe protein is physically cleaved after Arginine 172

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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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M Na Citrate, 30% PEG 6000, 2M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→43.9 Å / Num. obs: 54597 / % possible obs: 88.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.087 / Rsym value: 0.075 / Net I/σ(I): 21.8
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.774 / % possible all: 44

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
RefinementResolution: 1.45→43.9 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.56
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2729 5 %random selection
Rwork0.1498 ---
obs0.1513 54597 88.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.45→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 441 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112804
X-RAY DIFFRACTIONf_angle_d1.2993826
X-RAY DIFFRACTIONf_dihedral_angle_d11.6991000
X-RAY DIFFRACTIONf_chiral_restr0.055434
X-RAY DIFFRACTIONf_plane_restr0.007483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4479-1.47420.2794700.24461341X-RAY DIFFRACTION44
1.4742-1.50260.2347840.22331636X-RAY DIFFRACTION54
1.5026-1.53320.2184900.2071932X-RAY DIFFRACTION63
1.5332-1.56660.21351340.18032270X-RAY DIFFRACTION75
1.5666-1.6030.20021520.17792740X-RAY DIFFRACTION91
1.603-1.64310.20371630.1732942X-RAY DIFFRACTION97
1.6431-1.68750.20561570.16742945X-RAY DIFFRACTION97
1.6875-1.73720.21031670.16512929X-RAY DIFFRACTION97
1.7372-1.79330.18841810.16412941X-RAY DIFFRACTION97
1.7933-1.85740.16771380.16122899X-RAY DIFFRACTION95
1.8574-1.93170.21871460.15913003X-RAY DIFFRACTION98
1.9317-2.01960.18741480.15252988X-RAY DIFFRACTION98
2.0196-2.12610.16641710.14222987X-RAY DIFFRACTION98
2.1261-2.25930.18791500.14132944X-RAY DIFFRACTION96
2.2593-2.43380.17361690.14992990X-RAY DIFFRACTION98
2.4338-2.67870.17671390.14953066X-RAY DIFFRACTION99
2.6787-3.06620.15311450.14893010X-RAY DIFFRACTION97
3.0662-3.86270.16911570.13063110X-RAY DIFFRACTION99
3.8627-43.91620.16371680.13623195X-RAY DIFFRACTION98

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