[English] 日本語
Yorodumi
- PDB-5jts: Structure of a beta-1,4-mannanase, SsGH134. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jts
TitleStructure of a beta-1,4-mannanase, SsGH134.
Componentsbeta-1,4-mannanase
KeywordsHYDROLASE / beta-1 / 4-mannanase / carbohydrate degrading / glycosyl hydrolase
Function / homology: / Glycosyl hydrolase family 134 / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / Beta-1,4-mannanase
Function and homology information
Biological speciesStreptomyces sp. nrrl B-244 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsJin, Y. / Petricevic, M. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
Funding support United Kingdom, Australia, 2items
OrganizationGrant numberCountry
Eupropean Research CouncilAdG-322942 United Kingdom
Australian Research Council Australia
CitationJournal: ACS Cent Sci / Year: 2016
Title: A beta-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.
Authors: Jin, Y. / Petricevic, M. / John, A. / Raich, L. / Jenkins, H. / Portela De Souza, L. / Cuskin, F. / Gilbert, H.J. / Rovira, C. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Oct 30, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3796
Polymers18,0051
Non-polymers3745
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.910, 53.680, 81.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein beta-1,4-mannanase


Mass: 18004.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Streptomyces sp. NRRL B-24484, Taxonomy ID: 1463833
Source: (gene. exp.) Streptomyces sp. nrrl B-244 (bacteria) / Strain: NRRL B-24484 / Plasmid: pHisMALP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus
References: UniProt: A0A1L1QK12*PLUS, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein stock in the buffer of 20 mM sodium phosphate, pH7.2, and 200 mM NaCl is mixed 1:1 with the precipitant consist of 20 % PEG6000, 0.15-0.2 M CaCl2,and 0.1 M Na HEPES, pH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.09→33.62 Å / Num. obs: 68246 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 6.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.2
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.532 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha-helical fragment

Resolution: 1.09→33.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.88 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16316 3439 5 %RANDOM
Rwork0.13913 ---
obs0.14039 64732 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.314 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20 Å2
2---0.48 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.09→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 23 150 1385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191289
X-RAY DIFFRACTIONr_bond_other_d0.0020.021158
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9331751
X-RAY DIFFRACTIONr_angle_other_deg1.03832663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30624.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55915186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.366156
X-RAY DIFFRACTIONr_chiral_restr0.1160.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021552
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02320
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3511.254673
X-RAY DIFFRACTIONr_mcbond_other1.3541.249672
X-RAY DIFFRACTIONr_mcangle_it1.7881.888843
X-RAY DIFFRACTIONr_mcangle_other1.7871.89844
X-RAY DIFFRACTIONr_scbond_it1.6391.413616
X-RAY DIFFRACTIONr_scbond_other1.6381.413616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9962.065902
X-RAY DIFFRACTIONr_long_range_B_refined3.01811.3491647
X-RAY DIFFRACTIONr_long_range_B_other3.01711.3561648
X-RAY DIFFRACTIONr_rigid_bond_restr2.07332447
X-RAY DIFFRACTIONr_sphericity_free25.882554
X-RAY DIFFRACTIONr_sphericity_bonded9.23652514
LS refinement shellResolution: 1.09→1.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 230 -
Rwork0.277 4762 -
obs--99.84 %

+
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