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- PDB-9ojl: Crystal Structure of GH18 Chitinase Domain from Vibrio splendidus -

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Basic information

Entry
Database: PDB / ID: 9ojl
TitleCrystal Structure of GH18 Chitinase Domain from Vibrio splendidus
ComponentsChitinase
KeywordsHYDROLASE / Glycoside Hydrolase Family 18 / GH18 / Exochitinase / Endochitinase
Function / homology
Function and homology information


chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / GlcNAc-binding protein A, third domain / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / : / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site ...: / GlcNAc-binding protein A, third domain / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / : / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chitinase
Similarity search - Component
Biological speciesVibrio splendidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHorton, J.G. / Jackson, C.J. / Frkic, R.L.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Crystal Structure of GH18 Chitinase Domain from Vibrio splendidus
Authors: Horton, J.G. / Jackson, C.J. / Frkic, R.L.
History
DepositionMay 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
C: Chitinase
D: Chitinase
E: Chitinase
F: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,85533
Polymers224,8776
Non-polymers1,97827
Water43,2362400
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8686
Polymers37,4791
Non-polymers3885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8686
Polymers37,4791
Non-polymers3885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9928
Polymers37,4791
Non-polymers5137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8246
Polymers37,4791
Non-polymers3445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6383
Polymers37,4791
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6664
Polymers37,4791
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.918, 154.033, 156.602
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
Chitinase


Mass: 37479.430 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Catalytic domain of A0A837NXJ2. Addition of custom Sec signal peptide on N-terminal. Signal peptide cleaved during translocation between Ala21/Ala22. C-terminal LEHHHHHH. Modeled residues Pro26 to Gly342
Source: (gene. exp.) Vibrio splendidus (bacteria) / Gene: AN168_05695 / Plasmid: pET-29b(+)
Details (production host): Strain has IPTG-inducible T7 RNA polymerase cassette
Production host: Vibrio natriegens (bacteria) / Strain (production host): Vmax Express / References: UniProt: A0A837NXJ2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2400 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M NaCl, 0.1M Bis-Tris 7.0, 1.7M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→49.44 Å / Num. obs: 245129 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.056 / Rrim(I) all: 0.209 / Χ2: 1 / Net I/σ(I): 10.7 / Num. measured all: 3404026
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 2.092 / Num. measured all: 165627 / Num. unique obs: 11996 / CC1/2: 0.358 / Rpim(I) all: 0.582 / Rrim(I) all: 2.172 / Χ2: 0.99 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.44 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 12202 4.98 %
Rwork0.1693 --
obs0.1713 244980 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15032 0 122 2400 17554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01615694
X-RAY DIFFRACTIONf_angle_d1.29521369
X-RAY DIFFRACTIONf_dihedral_angle_d14.3995597
X-RAY DIFFRACTIONf_chiral_restr0.0872224
X-RAY DIFFRACTIONf_plane_restr0.0112854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.34883800.3227689X-RAY DIFFRACTION100
1.82-1.840.33563750.30697723X-RAY DIFFRACTION100
1.84-1.860.33214210.28997685X-RAY DIFFRACTION100
1.86-1.890.31084640.26987628X-RAY DIFFRACTION100
1.89-1.910.28994140.25597669X-RAY DIFFRACTION100
1.91-1.940.26993520.24017726X-RAY DIFFRACTION100
1.94-1.970.25714130.23167722X-RAY DIFFRACTION100
1.97-20.30074110.23257714X-RAY DIFFRACTION100
2-2.030.26514160.22237677X-RAY DIFFRACTION100
2.03-2.060.24794680.21417660X-RAY DIFFRACTION100
2.06-2.10.23224230.20267659X-RAY DIFFRACTION100
2.1-2.130.23754110.18617717X-RAY DIFFRACTION100
2.13-2.180.22174460.187718X-RAY DIFFRACTION100
2.18-2.220.21624150.17087664X-RAY DIFFRACTION100
2.22-2.270.23743630.17417768X-RAY DIFFRACTION100
2.27-2.320.21153900.17037738X-RAY DIFFRACTION100
2.32-2.380.21533760.16717763X-RAY DIFFRACTION100
2.38-2.440.21283880.16767787X-RAY DIFFRACTION100
2.44-2.510.22184100.16817711X-RAY DIFFRACTION100
2.51-2.60.20774280.16327737X-RAY DIFFRACTION100
2.6-2.690.22594160.1697737X-RAY DIFFRACTION100
2.69-2.80.22913850.17017803X-RAY DIFFRACTION100
2.8-2.920.21083820.16067793X-RAY DIFFRACTION100
2.92-3.080.20524260.15997769X-RAY DIFFRACTION100
3.08-3.270.22443800.16857846X-RAY DIFFRACTION100
3.27-3.520.19823830.15317819X-RAY DIFFRACTION100
3.52-3.880.16383890.13737858X-RAY DIFFRACTION100
3.88-4.440.15634390.12147866X-RAY DIFFRACTION100
4.44-5.590.16024120.12197950X-RAY DIFFRACTION100
5.59-49.440.15934260.14918182X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 50.7676 Å / Origin y: -3.9614 Å / Origin z: -19.2532 Å
111213212223313233
T0.1657 Å20.0138 Å20.0052 Å2-0.1417 Å20.0231 Å2--0.1473 Å2
L0.0738 °2-0.0327 °20.0051 °2-0.1623 °2-0.0583 °2--0.189 °2
S-0.0295 Å °-0.0052 Å °0.0124 Å °-0.0157 Å °-0.03 Å °-0.0969 Å °-0.0036 Å °0.0459 Å °0.0514 Å °
Refinement TLS groupSelection details: all

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