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- PDB-6u4z: Crystal Structure of a family 76 glycoside hydrolase from a bovin... -

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Basic information

Entry
Database: PDB / ID: 6u4z
TitleCrystal Structure of a family 76 glycoside hydrolase from a bovine Bacteroides thetaiotaomicron strain
ComponentsAlpha-1,6-mannanase
KeywordsHYDROLASE / Carbohydrate / GH76
Function / homologycellobiose epimerase activity / : / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / carbohydrate metabolic process / hydrolase activity / Alpha-1,6-mannanase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsJones, D.R. / Abbott, D.W.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Analysis of Active Site Architecture and Reaction Product Linkage Chemistry Reveals a Conserved Cleavage Substrate for an Endo-alpha-mannanase within Diverse Yeast Mannans.
Authors: Jones, D.R. / Xing, X. / Tingley, J.P. / Klassen, L. / King, M.L. / Alexander, T.W. / Abbott, D.W.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: Alpha-1,6-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4233
Polymers58,0791
Non-polymers3442
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.420, 58.520, 159.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-1,6-mannanase / Cellobiose 2-epimerase


Mass: 58078.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: Btheta7330_05006, DW011_13140 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0P0FW82, cellobiose epimerase
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% (w/v) PEG 1500, 100mM Sodium chloride, and 100mM Bis-TRIS-Propane pH 8.2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→47.137 Å / Num. obs: 102646 / % possible obs: 99.95 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0589 / Rrim(I) all: 0.068 / Χ2: 1.075 / Net I/σ(I): 16.62 / Num. measured all: 847371
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.456.3090.5463.2599700.8460.59699.8
1.45-1.56.6350.3874.7797400.9240.4299.9
1.5-1.566.8210.2866.5992840.9580.309100
1.56-1.636.9890.2158.6689810.9790.233100
1.63-1.717.130.16911.1285470.9860.182100
1.71-1.87.1790.12814.5381540.9910.138100
1.8-1.917.120.10217.8377690.9940.111100
1.91-2.057.0170.08221.8572590.9950.08999.9
2.05-2.216.8690.0725.0768010.9960.07699.9
2.21-2.426.7970.06327.162820.9960.06899.9
2.42-2.716.8040.05728.9756940.9970.06299.9
2.71-3.126.830.05130.7450640.9980.05599.9
3.12-3.836.8770.04332.3543150.9990.04799.9
3.83-5.416.9530.03533.5233950.9990.03799.9
5.41-47.1376.6160.03332.5919710.9970.03699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C1S

4c1s


Resolution: 1.4→47.137 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.25
RfactorNum. reflection% reflection
Rfree0.1953 5133 5 %
Rwork0.1801 --
obs0.1809 102646 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.43 Å2 / Biso mean: 17.9868 Å2 / Biso min: 9.44 Å2
Refinement stepCycle: final / Resolution: 1.4→47.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 23 370 4149
Biso mean--30.3 24.01 -
Num. residues----473
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.41590.28141700.24473235
1.4159-1.43260.24921680.23333185
1.4326-1.450.23021690.21693199
1.45-1.46840.21781700.20923235
1.4684-1.48770.23461680.19873191
1.4877-1.50810.21711690.19983218
1.5081-1.52960.23851690.18423207
1.5296-1.55250.21071700.19273228
1.5525-1.57670.19191700.1773242
1.5767-1.60260.20621680.17993183
1.6026-1.63020.1891710.18173254
1.6302-1.65990.18361680.17963188
1.6599-1.69180.20281700.1793234
1.6918-1.72630.21441710.19583238
1.7263-1.76390.21941690.18753218
1.7639-1.80490.21681700.18913223
1.8049-1.850.22381710.18693251
1.85-1.90010.22191710.18513248
1.9001-1.9560.23111690.18553222
1.956-2.01910.20431720.18443264
2.0191-2.09130.19141700.18313226
2.0913-2.1750.20721720.18253265
2.175-2.2740.20751700.18323234
2.274-2.39390.20561720.17533270
2.3939-2.54390.19841730.18263282
2.5439-2.74030.19051720.18333270
2.7403-3.0160.19341740.18463301
3.016-3.45230.18321750.183327
3.4523-4.3490.16051760.16093344
4.349-47.1370.17111860.16153531

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