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- PDB-5ylh: Structure of GH113 beta-1,4-mannanase -

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Basic information

Entry
Database: PDB / ID: 5ylh
TitleStructure of GH113 beta-1,4-mannanase
Componentsbeta-1,4-mannanase
KeywordsHYDROLASE / beta-1 / 4-mannanase
Function / homology: / Glycoside Hydrolase Family 113 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 1,4-beta-xylanase
Function and homology information
Biological speciesAmphibacillus xylanus NBRC 15112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsJiang, Z.Q. / You, X. / Yang, S.Q. / Huang, P. / Ma, J.W.
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase from Amphibacillus xylanus
Authors: You, X. / Qin, Z. / Yan, Q. / Yang, S. / Li, Y. / Jiang, Z.
#1: Journal: To Be Published
Title: Structure of GH113 beta-1,4-mannanase at 2.3 Angstroms resolution
Authors: Jiang, Z.Q. / You, X. / Yang, S.Q. / Huang, P. / Ma, J.W.
History
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,5632
Polymers72,5632
Non-polymers00
Water2,882160
1
A: beta-1,4-mannanase


Theoretical massNumber of molelcules
Total (without water)36,2821
Polymers36,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-1,4-mannanase


Theoretical massNumber of molelcules
Total (without water)36,2821
Polymers36,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.821, 69.375, 188.911
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 beta-1,4-mannanase


Mass: 36281.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphibacillus xylanus NBRC 15112 (bacteria)
Strain: NBRC 15112 / Gene: AXY_22370 / Production host: Escherichia coli (E. coli) / References: UniProt: K0J0N5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, HEPES Na, 2-Propylalcohol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.29→30.38 Å / Num. obs: 29076 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8
Reflection shellResolution: 2.29→30.383 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.118 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIXv1.12refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXv1.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIV

3civ


Resolution: 2.29→2.38 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2349 2000 6.91 %
Rwork0.1862 --
obs0.1897 29073 88 %
Refinement stepCycle: LAST / Resolution: 2.29→2.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5116 0 0 160 5276
LS refinement shellHighest resolution: 2.29 Å

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