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- PDB-6k7z: Crystal structure of a GH18 chitinase from Pseudoalteromonas aurantia -

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Basic information

Entry
Database: PDB / ID: 6k7z
TitleCrystal structure of a GH18 chitinase from Pseudoalteromonas aurantia
ComponentsGH18 chiitnase
KeywordsHYDROLASE / Chitinase / GH18 / Carbohydrate
Function / homology
Function and homology information


chitinase / chitinase activity / chitin binding / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesPseudoalteromonas aurantia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsWang, Y.J. / Li, P.Y. / Cao, H.Y. / Chen, X.L. / Zhang, Y.Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)91851205 China
National Science Foundation (China)41676180 China
National Science Foundation (China)91751101 China
CitationJournal: Front Microbiol / Year: 2019
Title: Structural Insight Into Chitin Degradation and Thermostability of a Novel Endochitinase From the Glycoside Hydrolase Family 18.
Authors: Wang, Y.J. / Jiang, W.X. / Zhang, Y.S. / Cao, H.Y. / Zhang, Y. / Chen, X.L. / Li, C.Y. / Wang, P. / Zhang, Y.Z. / Song, X.Y. / Li, P.Y.
History
DepositionJun 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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
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: GH18 chiitnase
B: GH18 chiitnase
C: GH18 chiitnase
D: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)126,2364
Polymers126,2364
Non-polymers00
Water17,853991
1
A: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.618, 87.486, 88.836
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
GH18 chiitnase


Mass: 31559.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas aurantia (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A650AJ72*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 8000, 0.05 M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 96262 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 30.3
Reflection shellResolution: 1.799→1.863 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 10.2 / Num. unique obs: 9086

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSJ

2gsj


Resolution: 1.799→33.019 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 46.81
RfactorNum. reflection% reflection
Rfree0.2372 4511 4.72 %
Rwork0.2121 --
obs0.2133 95543 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.799→33.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 0 991 9439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068704
X-RAY DIFFRACTIONf_angle_d0.84311872
X-RAY DIFFRACTIONf_dihedral_angle_d11.5585168
X-RAY DIFFRACTIONf_chiral_restr0.0531320
X-RAY DIFFRACTIONf_plane_restr0.0061560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7992-1.81960.30791270.26052535X-RAY DIFFRACTION82
1.8196-1.8410.32221450.26223008X-RAY DIFFRACTION100
1.841-1.86350.29631350.25263120X-RAY DIFFRACTION100
1.8635-1.8870.26491370.25733078X-RAY DIFFRACTION100
1.887-1.91190.23341020.24923095X-RAY DIFFRACTION100
1.9119-1.93810.26161350.24983055X-RAY DIFFRACTION100
1.9381-1.96570.24911590.23543011X-RAY DIFFRACTION99
1.9657-1.99510.24481520.23693068X-RAY DIFFRACTION100
1.9951-2.02620.24551480.23163091X-RAY DIFFRACTION100
2.0262-2.05950.21791540.23873069X-RAY DIFFRACTION100
2.0595-2.0950.24971590.2283039X-RAY DIFFRACTION100
2.095-2.13310.21861440.22373050X-RAY DIFFRACTION99
2.1331-2.17410.2671490.22583042X-RAY DIFFRACTION100
2.1741-2.21840.22521560.22253097X-RAY DIFFRACTION100
2.2184-2.26670.24951450.22273058X-RAY DIFFRACTION100
2.2667-2.31940.22061550.21893027X-RAY DIFFRACTION99
2.3194-2.37740.20531410.22473068X-RAY DIFFRACTION99
2.3774-2.44160.28891480.22083080X-RAY DIFFRACTION100
2.4416-2.51350.26621630.21813022X-RAY DIFFRACTION99
2.5135-2.59460.26921700.20213031X-RAY DIFFRACTION99
2.5946-2.68720.24831520.20583066X-RAY DIFFRACTION100
2.6872-2.79480.23981690.20513042X-RAY DIFFRACTION100
2.7948-2.92190.23181880.21453028X-RAY DIFFRACTION99
2.9219-3.07590.1841780.20593034X-RAY DIFFRACTION99
3.0759-3.26840.23021670.20573049X-RAY DIFFRACTION99
3.2684-3.52050.21741590.20463020X-RAY DIFFRACTION99
3.5205-3.87430.23081370.20243078X-RAY DIFFRACTION98
3.8743-4.43380.23181420.17823083X-RAY DIFFRACTION99
4.4338-5.58170.22361670.17833077X-RAY DIFFRACTION99
5.5817-33.02430.23511280.19362911X-RAY DIFFRACTION91

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