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- PDB-5dyn: B. fragilis cysteine protease -

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Basic information

Entry
Database: PDB / ID: 5dyn
TitleB. fragilis cysteine protease
Components(Putative peptidase) x 2
KeywordsHYDROLASE / cysteine protease / enzyme / cleavage
Function / homologyRossmann fold - #11970 / Peptidase C11, clostripain / Clostripain family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Peptidase
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsChoi, V.M. / Herrou, J. / Hecht, A.L. / Turner, J.R. / Crosson, S. / Bubeck Wardenburg, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007281 United States
Department of Pediatrics and Pilot and Feasibility Awrad from the Digestive Diseases Research Core Center- University of ChicagoNIDDK P30DK42086 United States
CitationJournal: Nat. Med. / Year: 2016
Title: Activation of Bacteroides fragilis toxin by a novel bacterial protease contributes to anaerobic sepsis in mice.
Authors: Choi, V.M. / Herrou, J. / Hecht, A.L. / Teoh, W.P. / Turner, J.R. / Crosson, S. / Bubeck Wardenburg, J.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peptidase
B: Putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,35611
Polymers43,1362
Non-polymers2199
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-33 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.320, 48.900, 60.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative peptidase


Mass: 14413.295 Da / Num. of mol.: 1 / Fragment: UNP residues 7-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 43859 / Gene: BF9343_2671 / Plasmid: Pet28 / Details (production host): KanR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): Rosetta / References: UniProt: Q5LBR6
#2: Protein Putative peptidase


Mass: 28722.865 Da / Num. of mol.: 1 / Fragment: UNP residues 135-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 43859 / Gene: BF9343_2671 / Plasmid: Pet28 / Details (production host): KanR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): Rosetta / References: UniProt: Q5LBR6
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 200 mM Ammonium Citrate Dibasic (pH 5), 25% (w/v) pEG3350
PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.48→38.43 Å / Num. obs: 13750 / % possible obs: 99.93 % / Redundancy: 7.22 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.88
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.58 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
XDSdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UWS

3uws


Resolution: 2.48→38.43 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 689 5.01 %
Rwork0.1751 --
obs0.1775 13750 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 9 50 2933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032967
X-RAY DIFFRACTIONf_angle_d0.694033
X-RAY DIFFRACTIONf_dihedral_angle_d12.6391073
X-RAY DIFFRACTIONf_chiral_restr0.025419
X-RAY DIFFRACTIONf_plane_restr0.003523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4801-2.67160.32281470.22622544X-RAY DIFFRACTION100
2.6716-2.94030.2791260.21042569X-RAY DIFFRACTION100
2.9403-3.36560.25091600.18572563X-RAY DIFFRACTION100
3.3656-4.23940.20171310.1562611X-RAY DIFFRACTION100
4.2394-38.40.17391250.16062774X-RAY DIFFRACTION100

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