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- PDB-5jvk: Structural insights into a family 39 glycoside hydrolase from the... -

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Basic information

Entry
Database: PDB / ID: 5jvk
TitleStructural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2.
ComponentsUncharacterized protein
KeywordsHYDROLASE / Bacteroides / GH39 / phylogeny / Endo-glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
T9SS C-terminal target domain-containing protein
Similarity search - Component
Biological speciesBacteroides cellulosilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsAli-Ahmad, A. / Garron, M.L. / Zamboni, V. / Lenfant, N. / Bourne, Y. / Vincent, F.
Funding support France, 1items
OrganizationGrant numberCountry
Vaincre la mucoviscidose France
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2.
Authors: Ali-Ahmad, A. / Garron, M.L. / Zamboni, V. / Lenfant, N. / Nurizzo, D. / Henrissat, B. / Berrin, J.G. / Bourne, Y. / Vincent, F.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,25919
Polymers194,5033
Non-polymers1,75616
Water9,674537
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2115
Polymers64,8341
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4366
Polymers64,8341
Non-polymers6025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6128
Polymers64,8341
Non-polymers7787
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.540, 157.540, 155.644
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 Uncharacterized protein


Mass: 64834.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus (bacteria)
Gene: BcellWH2_03314 / Plasmid: pDest17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A0N7IFL6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2 M AmSO4, 0.1 M CAPS pH 8 and 0.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726, 1.2543
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
21.25431
ReflectionResolution: 2.5→48.9 Å / Num. obs: 71297 / % possible obs: 92 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 14.5 / % possible all: 65.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.77 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.899 / SU ML: 0.208 / Cross valid method: FREE R-VALUE / ESU R: 0.403 / ESU R Free: 0.26 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24117 1429 2 %RANDOM
Rwork0.20641 ---
obs0.20711 69794 92.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.956 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.5→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11487 0 106 537 12130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211187
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.97216192
X-RAY DIFFRACTIONr_angle_other_deg0.865325810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72351467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56224.767516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.829151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.411548
X-RAY DIFFRACTIONr_chiral_restr0.0650.21806
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022603
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0093.7015877
X-RAY DIFFRACTIONr_mcbond_other1.0093.75876
X-RAY DIFFRACTIONr_mcangle_it1.8685.5487341
X-RAY DIFFRACTIONr_mcangle_other1.8685.5487342
X-RAY DIFFRACTIONr_scbond_it0.6683.7315999
X-RAY DIFFRACTIONr_scbond_other0.6683.7315999
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2775.558852
X-RAY DIFFRACTIONr_long_range_B_refined3.63528.07412996
X-RAY DIFFRACTIONr_long_range_B_other3.63528.07512997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 74 -
Rwork0.303 3349 -
obs--60.97 %

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