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

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Basic information

Entry
Database: PDB / ID: 6hze
TitleBP0997, GH138 enzyme targeting pectin rhamnogalacturonan II
ComponentsBPa0997
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 / beta-D-galactopyranuronic acid / BPa0997
Function and homology information
Biological speciesBacteroides paurosaccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: BPa0997
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,61014
Polymers204,9922
Non-polymers61812
Water00
1
A: BPa0997
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,87410
Polymers102,4961
Non-polymers3789
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BPa0997
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7364
Polymers102,4961
Non-polymers2403
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.498, 107.376, 139.211
Angle α, β, γ (deg.)90.00, 98.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BPa0997


Mass: 102495.898 Da / Num. of mol.: 2 / Mutation: E361S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides paurosaccharolyticus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8GZY5*PLUS
#2: 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
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 30 mM NaF, 30 mM NaBr, 30 mM NaI, 100 mM Imidazole/MES pH 6.5, 25 % MPD, 25 % PEG 1000 and 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→47.35 Å / Num. obs: 55515 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.992 / Net I/σ(I): 10.5
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4532 / CC1/2: 0.835 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.91 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.865 / SU B: 36.195 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28173 2728 4.9 %RANDOM
Rwork0.21339 ---
obs0.21667 52768 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.56 Å2
Baniso -1Baniso -2Baniso -3
1--4.56 Å20 Å21.01 Å2
2--4.48 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.7→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13926 0 36 0 13962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01314308
X-RAY DIFFRACTIONr_bond_other_d0.0030.01713143
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.6519366
X-RAY DIFFRACTIONr_angle_other_deg1.1811.58230557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.87851709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47222.954755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.798152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2921570
X-RAY DIFFRACTIONr_chiral_restr0.0650.21810
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215865
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023045
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_it0.1480.6626854
X-RAY DIFFRACTIONr_mcbond_other0.1480.6626853
X-RAY DIFFRACTIONr_mcangle_it0.2770.9938557
X-RAY DIFFRACTIONr_mcangle_other0.2770.9938558
X-RAY DIFFRACTIONr_scbond_it0.140.6797454
X-RAY DIFFRACTIONr_scbond_other0.1390.6797454
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2271.01710810
X-RAY DIFFRACTIONr_long_range_B_refined1.7197.51815747
X-RAY DIFFRACTIONr_long_range_B_other1.7197.50715745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 204 -
Rwork0.362 3861 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.18950.20320.06950.5322-0.07820.47050.0019-0.008-0.0377-0.0024-0.025-0.01720.04420.03630.02310.3170.01440.03450.0045-0.01280.450528.629210.078870.1563
20.5362-0.1070.11660.5249-0.31061.0584-0.0175-0.2832-0.01620.0140.00330.01760.011-0.11420.01420.4557-0.0720.03480.6777-0.00250.557719.2134-11.12354.9114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 893
2X-RAY DIFFRACTION2B23 - 893

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