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- PDB-5mvh: Glycoside Hydrolase BACCELL_00856 -

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Basic information

Entry
Database: PDB / ID: 5mvh
TitleGlycoside Hydrolase BACCELL_00856
ComponentsBACCELL_00856
KeywordsHYDROLASE / Rhamnosidase / Bacteroides / Beta-propeller
Function / homologyBNR repeat-containing family member / Sialidase superfamily / Neuraminidase
Function and homology information
Biological speciesBacteroides cellulosilyticus DSM 14838 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMunoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Henrissat, B. / Gilbert, H.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council322280 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unusual active site location and catalytic apparatus in a glycoside hydrolase family.
Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Henrissat, B. / Gilbert, H.J.
History
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 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

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Assembly

Deposited unit
A: BACCELL_00856


Theoretical massNumber of molelcules
Total (without water)49,7421
Polymers49,7421
Non-polymers00
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.842, 68.627, 52.880
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BACCELL_00856


Mass: 49742.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria)
Gene: BACCELL_00856 / Production host: Escherichia coli (E. coli) / References: UniProt: E2N9B1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 16% PEG4000, Sodium acetate 0.1M, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→68.6 Å / Num. obs: 112843 / % possible obs: 98.4 % / Redundancy: 3.3 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→52.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.139 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21352 1582 4.6 %RANDOM
Rwork0.16687 ---
obs0.16905 32663 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.574 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0 Å20.18 Å2
2---0.11 Å20 Å2
3---1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.8→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 0 449 3658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193326
X-RAY DIFFRACTIONr_bond_other_d0.0020.022847
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9174542
X-RAY DIFFRACTIONr_angle_other_deg0.95136590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.455406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96223.693176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09815507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7251523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
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_it1.0581.571600
X-RAY DIFFRACTIONr_mcbond_other1.0451.5691599
X-RAY DIFFRACTIONr_mcangle_it1.7122.3451999
X-RAY DIFFRACTIONr_mcangle_other1.7132.3472000
X-RAY DIFFRACTIONr_scbond_it1.2941.651726
X-RAY DIFFRACTIONr_scbond_other1.2941.6511727
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0012.4342538
X-RAY DIFFRACTIONr_long_range_B_refined5.57419.0153909
X-RAY DIFFRACTIONr_long_range_B_other4.96218.2523794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 104 -
Rwork0.288 2335 -
obs--95.12 %

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