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- PDB-5xtj: Mannanase(RmMan134A) -

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Basic information

Entry
Database: PDB / ID: 5xtj
TitleMannanase(RmMan134A)
ComponentsEndo beta-1,4-mannanase
KeywordsHYDROLASE / native protein
Function / homology: / Glycosyl hydrolase family 134 / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / Uncharacterized protein / Man134A
Function and homology information
Biological speciesRhizopus microsporus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsJiang, Z.Q. / You, X. / Huang, P.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Structural and biochemical insights into the substrate-binding mechanism of a novel glycoside hydrolase family 134 beta-mannanase.
Authors: You, X. / Qin, Z. / Li, Y.X. / Yan, Q.J. / Li, B. / Jiang, Z.Q.
History
DepositionJun 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,5742
Polymers36,5742
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-2 kcal/mol
Surface area13540 Å2
Unit cell
Length a, b, c (Å)49.259, 59.350, 123.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo beta-1,4-mannanase / Endo beta-1 / 4-mannanase


Mass: 18286.934 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: RMCBS344292_04886 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1NDE2, UniProt: A0A2U8ZTY7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-Hcl, tri-Sodium Citrate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→45.7 Å / Num. obs: 17836 / % possible obs: 97 % / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.5

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Processing

Software
NameVersionClassification
PHENIXdev-2474-000refinement
HKL-3000data processing
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→45.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2109 --
Rwork0.1726 --
obs-17836 97 %
Refinement stepCycle: LAST / Resolution: 2.22→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 0 214 2739
LS refinement shellHighest resolution: 2.22 Å

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