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- PDB-5d9p: Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzym... -

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Basic information

Entry
Database: PDB / ID: 5d9p
TitleCrystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14, in complex with an inhibitory N-bromoacetylglycosylamine derivative of 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: 1.8 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: B-1,4-endoglucanase
B: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2718
Polymers78,7752
Non-polymers4,4966
Water13,511750
1
A: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6364
Polymers39,3881
Non-polymers2,2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6364
Polymers39,3881
Non-polymers2,2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.192, 49.015, 85.972
Angle α, β, γ (deg.)76.39, 89.98, 66.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein B-1,4-endoglucanase


Mass: 39387.508 Da / Num. of mol.: 2
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)-N-acetyl-beta-D-glucopyranosylamine


Type: oligosaccharide / Mass: 1103.975 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,7,6/[a2122h-1b_1-5_1*NCC/3=O][a2122h-1b_1-5][a212h-1a_1-5]/1-2-2-2-3-3-3/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1NAc]{[(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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 28 mg/mL plus 6.6 mM EDTA, incubated 4 degrees overnight, then added 8M XXXG-NHCOCH2Br (inhibitor), incubated at 37 degrees for 3 h, then 0.5 microL of this solution was mixed with 0.5 ...Details: 28 mg/mL plus 6.6 mM EDTA, incubated 4 degrees overnight, then added 8M XXXG-NHCOCH2Br (inhibitor), incubated at 37 degrees for 3 h, then 0.5 microL of this solution was mixed with 0.5 microL of reservoir solution: 0.2 M calcium chloride, 20% (w/v) PEG3350. Cryoprotectant = paratone-N oil.

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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 SATURN A200 / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→31.921 Å / Num. obs: 60113 / % possible obs: 92.8 % / Redundancy: 1.9 % / Rsym value: 0.06 / Net I/σ(I): 11.47
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.13 / % possible all: 86.5

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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: 1.8→31.921 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1850 3.08 %Random selection
Rwork0.1633 ---
obs0.1646 60096 92.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→31.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5444 0 302 750 6496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085996
X-RAY DIFFRACTIONf_angle_d1.1898192
X-RAY DIFFRACTIONf_dihedral_angle_d12.5082484
X-RAY DIFFRACTIONf_chiral_restr0.046957
X-RAY DIFFRACTIONf_plane_restr0.0051016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84820.34961300.25864140X-RAY DIFFRACTION85
1.8482-1.90260.27911380.23824270X-RAY DIFFRACTION89
1.9026-1.9640.25841420.21174361X-RAY DIFFRACTION90
1.964-2.03420.22021370.18994356X-RAY DIFFRACTION91
2.0342-2.11560.24691360.19254443X-RAY DIFFRACTION92
2.1156-2.21190.21821410.18414459X-RAY DIFFRACTION92
2.2119-2.32850.25271440.18794511X-RAY DIFFRACTION93
2.3285-2.47430.21171450.17334503X-RAY DIFFRACTION94
2.4743-2.66530.24511440.16934585X-RAY DIFFRACTION94
2.6653-2.93330.21981430.17484592X-RAY DIFFRACTION95
2.9333-3.35740.21371490.1634633X-RAY DIFFRACTION96
3.3574-4.22840.15481500.13454661X-RAY DIFFRACTION97
4.2284-31.92620.15661510.12594732X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 1.9301 Å / Origin y: -24.6715 Å / Origin z: -27.2349 Å
111213212223313233
T0.1444 Å2-0.0049 Å20.0058 Å2-0.1653 Å2-0.0095 Å2--0.1756 Å2
L0.0642 °2-0.0765 °20.1104 °2-0.2983 °2-0.2796 °2--0.4746 °2
S0.0284 Å °-0.0065 Å °-0.0082 Å °-0.0112 Å °0.0015 Å °0.0243 Å °0.0235 Å °0.0158 Å °0 Å °
Refinement TLS groupSelection details: all

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