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- PDB-4mgs: BiXyn10A CBM1 APO -

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Basic information

Entry
Database: PDB / ID: 4mgs
TitleBiXyn10A CBM1 APO
ComponentsPutative glycosyl hydrolase family 10
KeywordsHYDROLASE / Endo-xylanase
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative glycosyl hydrolase family 10
Similarity search - Component
Biological speciesBacteroides intestinalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChekan, J.R. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes.
Authors: Zhang, M. / Chekan, J.R. / Dodd, D. / Hong, P.Y. / Radlinski, L. / Revindran, V. / Nair, S.K. / Mackie, R.I. / Cann, I.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Feb 28, 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: Putative glycosyl hydrolase family 10


Theoretical massNumber of molelcules
Total (without water)16,7531
Polymers16,7531
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.737, 90.659, 30.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-948-

HOH

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Components

#1: Protein Putative glycosyl hydrolase family 10


Mass: 16752.572 Da / Num. of mol.: 1 / Fragment: UNP residues 153-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis (bacteria) / Strain: DSM 17393 / Gene: BACINT_04215 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CET4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.5 M Ammonium Sulfate, 0.1 M Bicine, pH 9.0, 42 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→22.793 Å / Num. all: 14417 / Num. obs: 14363 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 21.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.38 / Num. unique all: 695 / % possible all: 100

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Processing

Software
NameClassification
MD2data collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→22.79 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 1437 10 %
Rwork0.1588 --
obs0.1616 14363 99.97 %
all-14417 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→22.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 0 190 1305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061153
X-RAY DIFFRACTIONf_angle_d1.0241557
X-RAY DIFFRACTIONf_dihedral_angle_d15.636414
X-RAY DIFFRACTIONf_chiral_restr0.073164
X-RAY DIFFRACTIONf_plane_restr0.004199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86520.29521380.20981235X-RAY DIFFRACTION100
1.8652-1.93980.2291420.18161280X-RAY DIFFRACTION100
1.9398-2.02810.20151410.16831275X-RAY DIFFRACTION100
2.0281-2.13490.22471400.15621259X-RAY DIFFRACTION100
2.1349-2.26850.19611430.15331286X-RAY DIFFRACTION100
2.2685-2.44350.20411430.16781280X-RAY DIFFRACTION100
2.4435-2.68910.19921420.16971286X-RAY DIFFRACTION100
2.6891-3.07740.18291450.16461304X-RAY DIFFRACTION100
3.0774-3.87410.16231470.1381325X-RAY DIFFRACTION100
3.8741-22.79450.14671560.15171396X-RAY DIFFRACTION100

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