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- PDB-6hzg: BP0997, GH138 enzyme targeting pectin rhamnogalacturonan II -

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Basic information

Entry
Database: PDB / ID: 6hzg
TitleBP0997, GH138 enzyme targeting pectin rhamnogalacturonan II
ComponentsBPa0997 N-ter E361S
KeywordsHYDROLASE / Rahmnogalacturonan II / pectin / glycoside hydrolase family 38
Function / homologyBeta-hexosaminidase-like, domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / carbohydrate metabolic process / hydrolase activity / alpha-D-galactopyranuronic acid / beta-D-galactopyranuronic acid / BPa0997
Function and homology information
Biological speciesBacteroides paurosaccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBasle, A. / Cartmell, A. / Labourel, A. / Gilbert, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council322820 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural and functional analyses of glycoside hydrolase 138 enzymes targeting chain A galacturonic acid in the complex pectin rhamnogalacturonan II.
Authors: Labourel, A. / Basle, A. / Munoz-Munoz, J. / Ndeh, D. / Booth, S. / Nepogodiev, S.A. / Field, R.A. / Cartmell, A.
History
DepositionOct 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 15, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BPa0997 N-ter E361S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1376
Polymers102,4961
Non-polymers6415
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-26 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.298, 68.379, 220.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BPa0997 N-ter E361S


Mass: 102495.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides paurosaccharolyticus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8GZY5*PLUS

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 771 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 16 % PEG 8000, 100 mM Tris pH 8.4, 9% Butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.6→73.39 Å / Num. obs: 100505 / % possible obs: 90.5 % / Redundancy: 5.1 % / Net I/σ(I): 5.9
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.7 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
pointlessdata scaling
PHASERphasing
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→55.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.42 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 5047 5 %RANDOM
Rwork0.154 ---
obs0.156 95323 90.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2---2.66 Å20 Å2
3---3.84 Å2
Refinement stepCycle: LAST / Resolution: 1.6→55.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 41 769 6387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135829
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175214
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6517926
X-RAY DIFFRACTIONr_angle_other_deg1.4531.57912094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52222.616302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25415962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2181529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021268
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_it2.911.8932807
X-RAY DIFFRACTIONr_mcbond_other2.8811.8922806
X-RAY DIFFRACTIONr_mcangle_it3.6162.8493515
X-RAY DIFFRACTIONr_mcangle_other3.6152.853516
X-RAY DIFFRACTIONr_scbond_it3.9652.0073022
X-RAY DIFFRACTIONr_scbond_other3.9662.0073022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5562.9434410
X-RAY DIFFRACTIONr_long_range_B_refined5.11222.967080
X-RAY DIFFRACTIONr_long_range_B_other5.11222.9477079
X-RAY DIFFRACTIONr_rigid_bond_restr10.004311043
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 310 -
Rwork0.29 6535 -
obs--84.67 %

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