[English] 日本語
Yorodumi
- PDB-1qnr: The 3-D structure of a Trichoderma reesei b-mannanase from glycos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qnr
TitleThe 3-D structure of a Trichoderma reesei b-mannanase from glycoside hydrolase family 5
ComponentsENDO-1,4-B-D-MANNANASE
KeywordsHYDROLASE / MANNANASE / TRICHODERMA REESEI / ANOMALOUS SCATTERING
Function / homology
Function and homology information


mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / disaccharide binding / cellulose binding / extracellular region
Similarity search - Function
Mannan endo-1,4-beta-mannosidase-like / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases ...Mannan endo-1,4-beta-mannosidase-like / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding 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
4beta-beta-mannobiose / Mannan endo-1,4-beta-mannosidase A
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å
AuthorsSabini, E. / Schubert, H. / Murshudov, G. / Wilson, K.S. / Siika-Aho, M. / Penttila, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The Three-Dimensional Structure of a Trichoderma Reesei Beta-Mannanase from Glycoside Hydrolase Family 5.
Authors: Sabini, E. / Schubert, H. / Murshudov, G. / Wilson, K.S. / Siika-Aho, M. / Penttila, M.
History
DepositionOct 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDO-1,4-B-D-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2559
Polymers37,7471
Non-polymers1,5078
Water8,899494
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.748, 54.922, 61.363
Angle α, β, γ (deg.)90.00, 111.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein ENDO-1,4-B-D-MANNANASE


Mass: 37747.137 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 28-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Strain: ALKO4330 / Cellular location (production host): SECRETED / Gene (production host): CBH1 PROMOTER / Production host: TRICHODERMA REESEI (fungus) / Strain (production host): ALKO4330
References: UniProt: Q99036, mannan endo-1,4-beta-mannosidase

-
Sugars , 2 types, 5 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose / 4beta-beta-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-mannobiose
DescriptorTypeProgram
DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 497 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %
Crystal growpH: 8.5 / Details: 2M AMMONIUM SULPHATE, 0.1M GLYCINE PH 8.5
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/mlenzyme1drop
210 mMTris-HCl1drop
32 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 50979 / % possible obs: 91.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 11.65 Å2 / Rsym value: 0.063 / Net I/σ(I): 17.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 / % possible all: 50.3
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 50.3 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.4→19.8 Å / SU B: 0.98717 / SU ML: 0.03887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06771 / ESU R Free: 0.0623
RfactorNum. reflection% reflectionSelection details
Rfree0.171 -5 %RANDOM
Rwork0.124 ---
obs-56363 91.2 %-
Displacement parametersBiso mean: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.685 Å20 Å20.039 Å2
2--0.742 Å20 Å2
3---0.933 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 96 494 3258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3032
X-RAY DIFFRACTIONp_mcangle_it2.9033
X-RAY DIFFRACTIONp_scbond_it2.7512
X-RAY DIFFRACTIONp_scangle_it3.4673
X-RAY DIFFRACTIONp_plane_restr0.0294
X-RAY DIFFRACTIONp_chiral_restr0.1550.15
X-RAY DIFFRACTIONp_singtor_nbd0.1620.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.37
X-RAY DIFFRACTIONp_staggered_tor11.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.720
X-RAY DIFFRACTIONp_special_tor015

+
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