[English] 日本語
Yorodumi
- PDB-5d9o: Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzym... -

+
Open data


ID or keywords:

Loading...

-
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 / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Secretion system C-terminal sorting domain / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Secretion system C-terminal sorting domain / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more