[English] 日本語
Yorodumi
- PDB-5xxa: beta-1,4-mannanase-SeMet-RmMan134A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xxa
Titlebeta-1,4-mannanase-SeMet-RmMan134A
Componentsendo-1,4-beta-mannanase
KeywordsHYDROLASE / protocolSeleno-methionine
Function / homology: / Glycosyl hydrolase family 134 / Uncharacterized protein
Function and homology information
Biological speciesRhizopus microsporus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsJiang, Z.Q. / You, X. / Yang, D. / Huang, P.
CitationJournal: To Be Published
Title: Structure of endo-1,4-beta-mannanase at 1.76 Angstroms resolution.
Authors: Jiang, Z.Q. / You, X. / Yang, D. / Huang, P.
History
DepositionJul 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: endo-1,4-beta-mannanase
B: endo-1,4-beta-mannanase


Theoretical massNumber of molelcules
Total (without water)36,7612
Polymers36,7612
Non-polymers00
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area13220 Å2
Unit cell
Length a, b, c (Å)49.614, 59.083, 124.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein endo-1,4-beta-mannanase


Mass: 18380.725 Da / Num. of mol.: 2 / Fragment: UNP residues 20-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus microsporus (fungus) / Gene: BCV71DRAFT_26579, RMCBS344292_04886 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1NDE2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-Hcl, tri-Sodium Citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→42.81 Å / Num. obs: 36268 / % possible obs: 98 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.1
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 27 / % possible all: 98.5

-
Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→42.81 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.193 2000 -
Rwork0.186 --
obs-36267 98 %
Refinement stepCycle: LAST / Resolution: 1.76→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 0 417 2883

+
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