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- PDB-6dht: Bacteroides ovatus GH9 Bacova_02649 -

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Basic information

Entry
Database: PDB / ID: 6dht
TitleBacteroides ovatus GH9 Bacova_02649
ComponentsXyloglucan-specific endo-beta-1,4-glucanase BoGH9A
KeywordsHYDROLASE / GH9 / cellulase
Function / homology
Function and homology information


symbiotic process benefiting host / xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / xyloglucan catabolic process / cellulase activity / cell outer membrane
Similarity search - Function
Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Six-hairpin glycosidase-like superfamily ...Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Xyloglucan-specific endo-beta-1,4-glucanase BoGH9A
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsKoropatkin, N.M. / Foley, M.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118475 United States
CitationJournal: J. Mol. Biol. / Year: 2019
Title: A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus.
Authors: Foley, M.H. / Dejean, G. / Hemsworth, G.R. / Davies, G.J. / Brumer, H. / Koropatkin, N.M.
History
DepositionMay 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xyloglucan-specific endo-beta-1,4-glucanase BoGH9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,04624
Polymers63,6151
Non-polymers1,43223
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-6 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.646, 50.406, 95.980
Angle α, β, γ (deg.)90.000, 109.000, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1135-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Xyloglucan-specific endo-beta-1,4-glucanase BoGH9A / Glycosyl hydrolase family protein 9A / BoGH9A


Mass: 63614.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02649 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A7LXT3, xyloglucan-specific endo-beta-1,4-glucanase

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Non-polymers , 7 types, 549 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus screen condition A2 (0.06 M magnesium chloride, 0.06 M calcium chloride, 0.1 M imidazole-MES, pH 6.5, 30% mix of ethylene glycol and PEG8000)
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 12, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.42→44.74 Å / Num. obs: 109840 / % possible obs: 98.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08118 / Rrim(I) all: 0.0879 / Net I/σ(I): 20.8
Reflection shellResolution: 1.42→1.471 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 9432 / CC1/2: 0.956 / % possible all: 84.59

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→44.736 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.21
RfactorNum. reflection% reflection
Rfree0.1973 1898 1.82 %
Rwork0.1677 --
obs0.1682 104416 93.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.67 Å2 / Biso mean: 25.4728 Å2 / Biso min: 9.78 Å2
Refinement stepCycle: final / Resolution: 1.42→44.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 206 526 5052
Biso mean--37.9 33.35 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114556
X-RAY DIFFRACTIONf_angle_d1.2826142
X-RAY DIFFRACTIONf_chiral_restr0.073642
X-RAY DIFFRACTIONf_plane_restr0.007798
X-RAY DIFFRACTIONf_dihedral_angle_d14.0421630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4195-1.4550.3114900.28365171526166
1.455-1.49430.27571110.25736328643981
1.4943-1.53830.28021280.246783691187
1.5383-1.5880.2291320.22337114724691
1.588-1.64470.25171360.21157256739294
1.6447-1.71060.24471420.20087490763296
1.7106-1.78840.20641400.20347583772397
1.7884-1.88270.2321440.19697668781298
1.8827-2.00070.26141440.19377745788999
2.0007-2.15520.22811430.182277517894100
2.1552-2.3720.18661460.167578257971100
2.372-2.71520.20771470.158178668013100
2.7152-3.42070.19461450.156478908035100
3.4207-44.75790.13911500.128380488198100

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