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- PDB-5xxa: beta-1,4-mannanase-SeMet-RmMan134A -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-Hcl, tri-Sodium Citrate

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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

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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

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