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- PDB-5b4s: Crystal Structure of GH80 chitosanase from Mitsuaria chitosanitabida -

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Basic information

Entry
Database: PDB / ID: 5b4s
TitleCrystal Structure of GH80 chitosanase from Mitsuaria chitosanitabida
ComponentsChitosanase
KeywordsHYDROLASE / CHITOSANASE / GLYCOSIDE HYDROLASE / CHITOSAN
Function / homology
Function and homology information


chitosanase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolase family 80, chitosanase / Glycosyl hydrolase family 80 of chitosanase A / Chitosanases families 46 and 80 active sites signature. / Glycoside hydrolase, family 46 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesMitsuaria chitosanitabida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKumasaka, T. / Yorinaga, Y. / Yamamoto, M. / Hamada, K. / Kawamukai, M.
CitationJournal: FEBS Lett. / Year: 2017
Title: Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida
Authors: Yorinaga, Y. / Kumasaka, T. / Yamamoto, M. / Hamada, K. / Kawamukai, M.
History
DepositionApr 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitosanase
B: Chitosanase


Theoretical massNumber of molelcules
Total (without water)71,3712
Polymers71,3712
Non-polymers00
Water12,250680
1
A: Chitosanase


Theoretical massNumber of molelcules
Total (without water)35,6861
Polymers35,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitosanase


Theoretical massNumber of molelcules
Total (without water)35,6861
Polymers35,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.879, 56.366, 207.081
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 Chitosanase


Mass: 35685.641 Da / Num. of mol.: 2 / Fragment: UNP residues 81-391 / Mutation: T128V
Source method: isolated from a genetically manipulated source
Details: Expression tag "MRGSHHHHHHTDPH" was attached to the N-terminus of the mature protein. Since the UniProt O82856 entry includes pre-pro sequence (1-80), the mature protein starts at 81th Ala residue.
Source: (gene. exp.) Mitsuaria chitosanitabida (bacteria) / Gene: choA / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: O82856
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, ammonium sulphate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 8, 2001
RadiationMonochromator: Diamond (400) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.75→43.66 Å / Num. obs: 61905 / % possible obs: 99.26 % / Redundancy: 7.2 % / Biso Wilson estimate: 14.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.74
Reflection shellResolution: 1.75→1.812 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 12.38 / % possible all: 98.65

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→43.659 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 3150 5.09 %
Rwork0.1596 --
obs0.1612 61904 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→43.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 0 680 5392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064870
X-RAY DIFFRACTIONf_angle_d1.0376627
X-RAY DIFFRACTIONf_dihedral_angle_d12.3481729
X-RAY DIFFRACTIONf_chiral_restr0.069717
X-RAY DIFFRACTIONf_plane_restr0.005866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77610.21411370.16822509X-RAY DIFFRACTION99
1.7761-1.80390.21191230.16342490X-RAY DIFFRACTION99
1.8039-1.83350.21571430.16662488X-RAY DIFFRACTION99
1.8335-1.86510.20261410.17142520X-RAY DIFFRACTION99
1.8651-1.8990.25311340.16892492X-RAY DIFFRACTION99
1.899-1.93550.21991350.16282528X-RAY DIFFRACTION99
1.9355-1.9750.20691370.15682504X-RAY DIFFRACTION99
1.975-2.0180.19361370.15932529X-RAY DIFFRACTION99
2.018-2.06490.21371280.16362539X-RAY DIFFRACTION99
2.0649-2.11650.18911580.16022461X-RAY DIFFRACTION99
2.1165-2.17380.18061290.152585X-RAY DIFFRACTION99
2.1738-2.23770.19691460.1472495X-RAY DIFFRACTION99
2.2377-2.30990.19581570.1522523X-RAY DIFFRACTION99
2.3099-2.39250.19761420.14872547X-RAY DIFFRACTION100
2.3925-2.48830.17141040.16042580X-RAY DIFFRACTION99
2.4883-2.60150.19231400.162564X-RAY DIFFRACTION100
2.6015-2.73870.20281340.17172581X-RAY DIFFRACTION100
2.7387-2.91020.19341390.16862549X-RAY DIFFRACTION100
2.9102-3.13490.17371450.16862571X-RAY DIFFRACTION100
3.1349-3.45020.19191480.16862599X-RAY DIFFRACTION99
3.4502-3.94920.18141460.15922590X-RAY DIFFRACTION100
3.9492-4.97440.16011060.13672695X-RAY DIFFRACTION100
4.9744-43.67270.19031410.16622815X-RAY DIFFRACTION100

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