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- PDB-9buf: Hydrolase domain of Chitinase 1 from Streptomyces venezuelae -

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Basic information

Entry
Database: PDB / ID: 9buf
TitleHydrolase domain of Chitinase 1 from Streptomyces venezuelae
ComponentsExochitinase 1
KeywordsHYDROLASE / chitinase / exochitinase / GH18 / hydrolase domain
Function / homology
Function and homology information


chitinase / polysaccharide binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / chitinase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDalton, J.A.T. / Smith, O.B. / Frkic, R.L. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Hydrolase domain of Chitinase 1 from Streptomyces venezuelae
Authors: Dalton, J.A.T. / Smith, O.B. / Frkic, R.L. / Jackson, C.J.
History
DepositionMay 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 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: Exochitinase 1
B: Exochitinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5655
Polymers65,3132
Non-polymers2513
Water9,818545
1
A: Exochitinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9084
Polymers32,6571
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exochitinase 1


Theoretical massNumber of molelcules
Total (without water)32,6571
Polymers32,6571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.529, 54.769, 144.421
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-571-

HOH

31A-722-

HOH

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Components

#1: Protein Exochitinase 1


Mass: 32656.680 Da / Num. of mol.: 2 / Fragment: hydrolase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Strain: ATCC 10712 / Gene: SVEN_2589 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2R3N3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30 % (w/v) PEG 2000 MME, 0.2 M Ammonium sulphate, 0.1 M Sodium acetate

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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: Apr 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→41.57 Å / Num. obs: 61279 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.101 / Rrim(I) all: 0.264 / Χ2: 0.99 / Net I/σ(I): 6.2 / Num. measured all: 416395
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 2.302 / Num. measured all: 23362 / Num. unique obs: 3341 / CC1/2: 0.504 / Rpim(I) all: 0.929 / Rrim(I) all: 2.485 / Χ2: 0.91 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→41.57 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 3160 5.16 %
Rwork0.1947 --
obs0.1967 61231 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 14 545 4866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.884
X-RAY DIFFRACTIONf_dihedral_angle_d5.694635
X-RAY DIFFRACTIONf_chiral_restr0.053701
X-RAY DIFFRACTIONf_plane_restr0.007789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.34781270.29742535X-RAY DIFFRACTION100
1.78-1.80.30671150.29542504X-RAY DIFFRACTION100
1.8-1.830.34371320.2952514X-RAY DIFFRACTION100
1.83-1.870.34191320.27462527X-RAY DIFFRACTION100
1.87-1.90.27681330.26792519X-RAY DIFFRACTION100
1.9-1.940.32051330.24752530X-RAY DIFFRACTION100
1.94-1.980.31931370.23852497X-RAY DIFFRACTION100
1.98-2.020.2391570.22282496X-RAY DIFFRACTION100
2.02-2.060.28661350.21782483X-RAY DIFFRACTION100
2.06-2.120.29451430.21532511X-RAY DIFFRACTION100
2.12-2.170.25651350.20992509X-RAY DIFFRACTION100
2.17-2.240.24681460.19852505X-RAY DIFFRACTION100
2.24-2.310.23321290.19472525X-RAY DIFFRACTION100
2.31-2.390.29861010.1972569X-RAY DIFFRACTION100
2.39-2.490.24121250.19892555X-RAY DIFFRACTION100
2.49-2.60.26281410.19782506X-RAY DIFFRACTION100
2.6-2.740.2281640.19042520X-RAY DIFFRACTION100
2.74-2.910.23771440.19172493X-RAY DIFFRACTION100
2.91-3.130.23611520.19712524X-RAY DIFFRACTION100
3.13-3.450.20421840.18242477X-RAY DIFFRACTION100
3.45-3.950.21861190.1682593X-RAY DIFFRACTION100
3.95-4.970.15711450.13792546X-RAY DIFFRACTION99
4.98-41.570.15441310.15882633X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.80470.87070.78494.39170.22691.8848-0.0946-0.01160.16570.21960.11790.1528-0.2914-0.2947-0.02170.21690.044-0.02130.1630.01740.0796-23.6477-16.9259-18.6595
21.23270.47740.19610.6944-0.09921.1509-0.0899-0.23840.18150.363-0.0037-0.0167-0.3315-0.08270.0920.37770.0325-0.06120.1643-0.02110.1694-15.4115-16.6177-6.5532
32.3212-1.25340.00051.5936-0.03782.2833-0.1398-0.19150.11990.28560.0375-0.0252-0.1786-0.00790.08220.3003-0.0079-0.06830.1528-0.02010.1273-13.6634-26.6765-0.6772
40.9367-0.1630.37910.9316-0.22171.8789-0.0281-0.0039-0.0485-0.02470.04880.04640.0198-0.1754-0.02270.1709-0.0038-0.02780.1222-0.00510.1204-20.3045-33.2396-17.7879
52.75361.46330.13022.10740.18771.64590.04040.259-0.0664-0.10620.0865-0.08790.09430.2628-0.12920.16790.0481-0.00690.24-0.04240.13877.0159-50.478-37.6325
61.79160.2886-0.68051.0267-0.42931.73090.1230.0707-0.1611-0.0811-0.0061-0.00630.20360.2074-0.11140.21550.0378-0.06750.1618-0.0510.15583.8311-57.5014-30.056
77.7322-3.6791-4.02323.75792.36294.1171-0.1965-0.2749-0.48920.41270.1550.02120.50510.20540.01480.35150.0073-0.08120.14050.00210.19470.4446-63.3957-19.3393
81.2359-0.24770.20522.95730.22921.37810.1355-0.0056-0.10360.2321-0.0868-0.07340.20530.0183-0.04460.1926-0.0107-0.03430.1466-0.01760.09963.2753-47.8322-17.0511
91.1804-0.05880.51371.7084-0.91653.05150.05780.0810.0995-0.04430.0162-0.06090.03460.2368-0.05570.1238-0.03240.00790.1441-0.02140.13269.77-37.3008-24.7921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 309 )
5X-RAY DIFFRACTION5chain 'B' and (resid 15 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 132 )
7X-RAY DIFFRACTION7chain 'B' and (resid 133 through 149 )
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 201 )
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 309 )

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