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- PDB-5d9n: Crystal structure of PbGH5A, a glycoside hydrolase family 5 membe... -

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Basic information

Entry
Database: PDB / ID: 5d9n
TitleCrystal structure of PbGH5A, a glycoside hydrolase family 5 member from Prevotella bryantii B14, in complex with the xyloglucan heptasaccharide XXXG
ComponentsB-1,4-endoglucanase
KeywordsHYDROLASE / endo-beta-glucanase/endo-xyloglucanase / GLYCOSYL HYDROLASE FAMILY 5 / MIXED ALPHA-BETA / TIM BARREL
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity / metal ion binding
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Secretion system C-terminal sorting domain / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Secretion system C-terminal sorting domain / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPrevotella bryantii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMorar, M. / Stogios, P.J. / Xu, X. / Cui, H. / Di Leo, R. / Yim, V. / Savchenko, A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure-Function Analysis of a Mixed-linkage beta-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B14.
Authors: McGregor, N. / Morar, M. / Fenger, T.H. / Stogios, P. / Lenfant, N. / Yin, V. / Xu, X. / Evdokimova, E. / Cui, H. / Henrissat, B. / Savchenko, A. / Brumer, H.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-1,4-endoglucanase
B: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1019
Polymers78,7752
Non-polymers2,3267
Water17,511972
1
A: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5715
Polymers39,3881
Non-polymers1,1834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5314
Polymers39,3881
Non-polymers1,1433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.560, 84.116, 138.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein B-1,4-endoglucanase


Mass: 39387.508 Da / Num. of mol.: 2 / Fragment: UNP residues 573-924
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella bryantii (bacteria) / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06842
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 microL of protein solution at 28 mg/mL mixed with 1.8 microL of reservoir solution (0.1 M sodium cacodylate pH 6.3 to 7.1, 0.2 M calcium acetate, 25% PEG8K), then soaking in reservoir ...Details: 1.8 microL of protein solution at 28 mg/mL mixed with 1.8 microL of reservoir solution (0.1 M sodium cacodylate pH 6.3 to 7.1, 0.2 M calcium acetate, 25% PEG8K), then soaking in reservoir solution supplemented with 20 mM XXXG. Cryoprotectant = paratone-N oil.
PH range: 6.3 - 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→24.866 Å / Num. obs: 74790 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rsym value: 0.067 / Net I/σ(I): 41.71
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 5.98 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VDH

3vdh


Resolution: 1.86→24.866 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1682 2000 2.68 %Random selection
Rwork0.1385 ---
obs0.1393 74720 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→24.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5462 0 149 972 6583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155894
X-RAY DIFFRACTIONf_angle_d1.378025
X-RAY DIFFRACTIONf_dihedral_angle_d13.0732253
X-RAY DIFFRACTIONf_chiral_restr0.075906
X-RAY DIFFRACTIONf_plane_restr0.0071023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90640.22231390.19435090X-RAY DIFFRACTION99
1.9064-1.9580.2441420.17945128X-RAY DIFFRACTION100
1.958-2.01560.19871410.16485129X-RAY DIFFRACTION100
2.0156-2.08060.20581410.15495138X-RAY DIFFRACTION100
2.0806-2.15490.17581420.14775151X-RAY DIFFRACTION100
2.1549-2.24110.1881410.14065122X-RAY DIFFRACTION100
2.2411-2.34310.17461430.13655172X-RAY DIFFRACTION100
2.3431-2.46650.20331410.13825173X-RAY DIFFRACTION100
2.4665-2.62090.18011430.14445191X-RAY DIFFRACTION100
2.6209-2.8230.17731430.14445186X-RAY DIFFRACTION100
2.823-3.10660.1531430.14425209X-RAY DIFFRACTION100
3.1066-3.5550.14011440.13265236X-RAY DIFFRACTION100
3.555-4.47460.14141460.11465302X-RAY DIFFRACTION100
4.4746-24.86790.15651510.13175493X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.159 Å / Origin y: 109.8212 Å / Origin z: 162.4227 Å
111213212223313233
T0.1798 Å2-0.0207 Å20.0129 Å2-0.1592 Å2-0.0167 Å2--0.1878 Å2
L0.5167 °2-0.1105 °20.1047 °2-0.2624 °2-0.0815 °2--0.6011 °2
S-0.0005 Å °-0.1106 Å °0.0415 Å °0.0632 Å °0.0114 Å °-0.0023 Å °-0.0373 Å °0.018 Å °-0.0098 Å °
Refinement TLS groupSelection details: all

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