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- PDB-5d9o: Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzym... -

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Basic information

Entry
Database: PDB / ID: 5d9o
TitleCrystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14, E280A mutant in complex with cellotetraose
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
beta-cellotetraose / B-1,4-endoglucanase
Similarity search - Component
Biological speciesPrevotella bryantii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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 / entity_name_com / 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_molecule_features / 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_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.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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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.ptnr1_symmetry / _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)80,1127
Polymers78,6592
Non-polymers1,4535
Water17,781987
1
A: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0764
Polymers39,3291
Non-polymers7473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-1,4-endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0363
Polymers39,3291
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.180, 85.058, 74.978
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein B-1,4-endoglucanase


Mass: 39329.473 Da / Num. of mol.: 2 / Mutation: E280A
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 beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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 crystals in ...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 crystals in reservoir solution supplemented with 10 mM cellotetraose for 2 h. 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: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→19.47 Å / Num. obs: 85184 / % possible obs: 97.1 % / Redundancy: 4 % / Rsym value: 0.082 / Net I/σ(I): 14
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.9 / % possible all: 94.1

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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: 1.55→19.456 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 4269 5.01 %Random selection
Rwork0.1525 ---
obs0.1539 85156 97.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→19.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 93 987 6520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075789
X-RAY DIFFRACTIONf_angle_d1.1187892
X-RAY DIFFRACTIONf_dihedral_angle_d12.2782152
X-RAY DIFFRACTIONf_chiral_restr0.046879
X-RAY DIFFRACTIONf_plane_restr0.0061014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56760.24451390.22692622X-RAY DIFFRACTION94
1.5676-1.5860.25811420.20382592X-RAY DIFFRACTION94
1.586-1.60540.25381530.19532528X-RAY DIFFRACTION94
1.6054-1.62570.22681320.1882663X-RAY DIFFRACTION95
1.6257-1.64710.25221520.182598X-RAY DIFFRACTION95
1.6471-1.66960.20751410.17482606X-RAY DIFFRACTION95
1.6696-1.69350.20791390.17042650X-RAY DIFFRACTION95
1.6935-1.71870.20481250.1662634X-RAY DIFFRACTION96
1.7187-1.74560.21321420.16842653X-RAY DIFFRACTION96
1.7456-1.77420.20651300.16922646X-RAY DIFFRACTION96
1.7742-1.80470.19621550.16432644X-RAY DIFFRACTION96
1.8047-1.83750.20461290.15652678X-RAY DIFFRACTION96
1.8375-1.87280.20571420.15592677X-RAY DIFFRACTION97
1.8728-1.9110.20471500.15952672X-RAY DIFFRACTION97
1.911-1.95260.19191350.15542702X-RAY DIFFRACTION97
1.9526-1.99790.19821600.1552664X-RAY DIFFRACTION97
1.9979-2.04780.18221270.1512751X-RAY DIFFRACTION98
2.0478-2.10310.18261460.15332678X-RAY DIFFRACTION98
2.1031-2.1650.19491490.14082712X-RAY DIFFRACTION98
2.165-2.23470.1731370.14482758X-RAY DIFFRACTION98
2.2347-2.31450.17361410.14972722X-RAY DIFFRACTION99
2.3145-2.4070.18771400.14632746X-RAY DIFFRACTION99
2.407-2.51630.18411400.14812740X-RAY DIFFRACTION99
2.5163-2.64870.16741480.14842791X-RAY DIFFRACTION99
2.6487-2.81420.17821210.15072774X-RAY DIFFRACTION100
2.8142-3.03070.16371220.15022795X-RAY DIFFRACTION100
3.0307-3.33430.13591550.14342784X-RAY DIFFRACTION100
3.3343-3.81370.13981660.13042772X-RAY DIFFRACTION100
3.8137-4.79290.14391490.13072803X-RAY DIFFRACTION100
4.7929-19.45750.17921620.15312832X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.1645 Å / Origin y: -17.5881 Å / Origin z: -43.8681 Å
111213212223313233
T0.0469 Å2-0.0005 Å20.0048 Å2-0.0445 Å2-0.0052 Å2--0.0601 Å2
L0.2323 °2-0.0333 °20.0267 °2-0.2164 °2-0.0579 °2--0.2984 °2
S0.0095 Å °0.0209 Å °-0.0039 Å °-0.0303 Å °-0.0028 Å °-0.0005 Å °-0.0023 Å °0.0017 Å °-0.0058 Å °
Refinement TLS groupSelection details: all

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