[English] 日本語
Yorodumi
- PDB-1uoz: Structure of the endoglucanase Cel6 from Mycobacterium tuberculos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uoz
TitleStructure of the endoglucanase Cel6 from Mycobacterium tuberculosis in complex with thiocellopentaose at 1.1 angstrom
ComponentsPUTATIVE CELLULASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 6
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulase activity / cellulose catabolic process / extracellular region / membrane
Similarity search - Function
1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-thio-beta-D-glucopyranose / : / Glucanase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsVarrot, A. / Leydier, S. / Pell, G. / Gilbert, H.J. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Mycobacterium Tuberculosis Strains Possess Functional Cellulases.
Authors: Varrot, A. / Leydier, S. / Pell, G. / Macdonald, J.M. / Stick, R.V. / Henrissat, B. / Gilbert, H.J. / Davies, G.J.
History
DepositionSep 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_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.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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1306
Polymers33,0841
Non-polymers1,0455
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.940, 92.627, 46.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2182-

HOH

21A-2314-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein PUTATIVE CELLULASE / ENDOGLUCANASE / CELA / RV0062 / MT0067 / MTV030.05


Mass: 33084.383 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 88-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: SYNTHETIC GENE / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI / References: UniProt: O53607, UniProt: Q79G13*PLUS

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose


Type: oligosaccharide / Mass: 568.700 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5_1*S][a2122h-1b_1-5][a2122h-1a_1-5]/1-2-3/a4-b1*S*_b4-c1*S*WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp4SH]{[(4+S)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-SGC / 4-thio-beta-D-glucopyranose / 4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE / 4-thio-beta-D-glucose / 4-thio-D-glucose / 4-thio-glucose


Type: D-saccharide, beta linking / Mass: 196.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5S
IdentifierTypeProgram
b-D-Glcp4SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 3 types, 498 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsA N-TERMINAL HIS TAG IS ATTACHED TO THE PROTEIN. THE FIRST 14 RESIDUES OF THE HIS TAG ARE NOT ...A N-TERMINAL HIS TAG IS ATTACHED TO THE PROTEIN. THE FIRST 14 RESIDUES OF THE HIS TAG ARE NOT VISIBLE IN DENSITY. ONLY THE CATALYTIC DOMAIN HAS BEEN CLONES CORRESPONDING TO RESIDUES 88 TO 380.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 38.81 %
Crystal growpH: 7.5
Details: 14 % PEG 4K, 100 MM HEPES 7.5, 200 MM LISO4. THE PROTEIN WAS AT 10MG/ML AND INCUBATED WITH 1 MM OF THIOCELLOPENTAOSE FOR 1HR PRIOR. CRYSTALLISATION. 20% GLYCEROL WAS ADDED AS CRYOPROTECTANT, pH 7.50

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.1→51.2 Å / Num. obs: 109101 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 17
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 7.9 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TML

1tml


Resolution: 1.1→51.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.237 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13 5464 5 %RANDOM
Rwork0.112 ---
obs0.113 103639 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.1→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 51 495 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212430
X-RAY DIFFRACTIONr_bond_other_d0.0030.022123
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9553330
X-RAY DIFFRACTIONr_angle_other_deg0.93834935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022795
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02511
X-RAY DIFFRACTIONr_nbd_refined0.2310.2562
X-RAY DIFFRACTIONr_nbd_other0.260.22560
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3181.51544
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93922466
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.473886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3634.5856
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.33222430
X-RAY DIFFRACTIONr_sphericity_free5.3552496
X-RAY DIFFRACTIONr_sphericity_bonded3.52122359
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.124 373
Rwork0.098 7565

+
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