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- PDB-5mum: Glycoside Hydrolase BACINT_00347 -

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Basic information

Entry
Database: PDB / ID: 5mum
TitleGlycoside Hydrolase BACINT_00347
ComponentsBACINT_00347
KeywordsHYDROLASE / Rhamnosidase / Bacteroides / Beta-propeller
Function / homologyBNR repeat-containing family member / Sialidase superfamily / Neuraminidase
Function and homology information
Biological speciesBacteroides intestinalis DSM 17393 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 Council322820 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 13, 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: Author supporting evidence / Data collection / Category: pdbx_audit_support / reflns_shell / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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: BACINT_00347
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4395
Polymers49,8381
Non-polymers6014
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint10 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.313, 68.438, 118.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein BACINT_00347


Mass: 49838.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria)
Gene: BACINT_00347 / Production host: Escherichia coli (E. coli) / References: UniProt: B3C613
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 and 200 mM Tri-potassium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→68.6 Å / Num. obs: 255841 / % 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
Starting model: 4IRT

4irt


Resolution: 1.8→68.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.495 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19096 1749 5 %RANDOM
Rwork0.15159 ---
obs0.15353 33250 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.636 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 1.8→68.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 28 314 3525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193355
X-RAY DIFFRACTIONr_bond_other_d0.0030.022887
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9194564
X-RAY DIFFRACTIONr_angle_other_deg0.9736672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89623.409176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09115510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1351526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023813
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02757
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_it1.0361.2341605
X-RAY DIFFRACTIONr_mcbond_other1.0331.2341604
X-RAY DIFFRACTIONr_mcangle_it1.7121.8392012
X-RAY DIFFRACTIONr_mcangle_other1.7111.842013
X-RAY DIFFRACTIONr_scbond_it1.6391.4041750
X-RAY DIFFRACTIONr_scbond_other1.6391.4041750
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5252.0242552
X-RAY DIFFRACTIONr_long_range_B_refined4.9815.1793981
X-RAY DIFFRACTIONr_long_range_B_other4.98115.1753981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 144 -
Rwork0.177 2401 -
obs--100 %

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