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- PDB-8xbd: GH18 family chitinase from cold seep metagenome -

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Basic information

Entry
Database: PDB / ID: 8xbd
TitleGH18 family chitinase from cold seep metagenome
ComponentsGH18 chitinase-like superfamily protein
KeywordsHYDROLASE / Glycoside hydrolase
Function / homology
Function and homology information


chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
GH18 chitinase-like superfamily protein
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Innov Geosci / Year: 2025
Title: Exploring the role of organotrophic microbes in geochemical cycling of cold seep sediments.
Authors: Chen, Y. / Yang, J. / Huang, X. / Zhang, J. / Li, Q. / Lyu, L. / Ju, F. / Li, J. / Zhang, S.
History
DepositionDec 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: GH18 chitinase-like superfamily protein
A: GH18 chitinase-like superfamily protein


Theoretical massNumber of molelcules
Total (without water)89,6382
Polymers89,6382
Non-polymers00
Water5,873326
1
B: GH18 chitinase-like superfamily protein


Theoretical massNumber of molelcules
Total (without water)44,8191
Polymers44,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GH18 chitinase-like superfamily protein


Theoretical massNumber of molelcules
Total (without water)44,8191
Polymers44,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.278, 114.286, 110.478
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

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Components

#1: Protein GH18 chitinase-like superfamily protein


Mass: 44819.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A142DUU5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M potassium bromide, 30% (w/v) polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Aug 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.4→19.09 Å / Num. obs: 33470 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.059 / Rrim(I) all: 0.144 / Χ2: 0.96 / Net I/σ(I): 9.3 / Num. measured all: 181837
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Num. measured all: 10362 / Num. unique obs: 3509 / CC1/2: 0.718 / Rpim(I) all: 0.366 / Rrim(I) all: 0.648 / Χ2: 0.92 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.09 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 1603 4.81 %
Rwork0.1995 --
obs0.2023 33316 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 0 326 6368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086184
X-RAY DIFFRACTIONf_angle_d0.9478402
X-RAY DIFFRACTIONf_dihedral_angle_d5.941836
X-RAY DIFFRACTIONf_chiral_restr0.051904
X-RAY DIFFRACTIONf_plane_restr0.0071094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.31520.24292876X-RAY DIFFRACTION100
2.48-2.570.27871590.22742886X-RAY DIFFRACTION100
2.57-2.670.29311360.20852894X-RAY DIFFRACTION100
2.67-2.790.24911210.19982895X-RAY DIFFRACTION100
2.79-2.940.30661390.20232888X-RAY DIFFRACTION100
2.94-3.120.25661470.19022909X-RAY DIFFRACTION100
3.12-3.360.28081230.19342909X-RAY DIFFRACTION100
3.36-3.690.26471170.20132902X-RAY DIFFRACTION99
3.69-4.220.24571670.22042736X-RAY DIFFRACTION96
4.22-5.30.21992100.16842860X-RAY DIFFRACTION100
5.3-19.090.23621320.1872958X-RAY DIFFRACTION100

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