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- PDB-8hrf: Catalytic domain of Vibrio parahaemolyticus chitinase 1 -

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Basic information

Entry
Database: PDB / ID: 8hrf
TitleCatalytic domain of Vibrio parahaemolyticus chitinase 1
ComponentsChitinase
KeywordsHYDROLASE / Chitinase
Function / homologyACETATE ION / :
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNakamura, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03094 Japan
CitationJournal: To Be Published
Title: Catalytic domain of Vibrio parahaemolyticus chitinase 1
Authors: Nakamura, A.
History
DepositionDec 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1927
Polymers123,9532
Non-polymers2385
Water12,845713
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0763
Polymers61,9771
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1164
Polymers61,9771
Non-polymers1393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.804, 159.996, 75.489
Angle α, β, γ (deg.)90.000, 92.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Chitinase


Mass: 61976.609 Da / Num. of mol.: 2 / Fragment: GH18 catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: BS585_05230 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E1IK76
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10% PEG 8000, 100 mM CaAc2, 100 mM Na-cacodylate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→28.7 Å / Num. obs: 39898 / % possible obs: 98.75 % / Redundancy: 7.2 % / Biso Wilson estimate: 14.18 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.63 / Num. unique obs: 3994 / % possible all: 97.42

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Processing

Software
NameVersionClassification
Coot1.20.1_4487model building
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.7 Å / SU ML: 0.3037 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2454 2021 5.12 %
Rwork0.1605 37420 -
obs0.1649 39441 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8692 0 11 713 9416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00778940
X-RAY DIFFRACTIONf_angle_d0.898112172
X-RAY DIFFRACTIONf_chiral_restr0.05081276
X-RAY DIFFRACTIONf_plane_restr0.00681608
X-RAY DIFFRACTIONf_dihedral_angle_d6.2511230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.27181430.16932643X-RAY DIFFRACTION97.34
2.56-2.630.31511380.17092607X-RAY DIFFRACTION97.37
2.63-2.710.29571450.18662682X-RAY DIFFRACTION98.36
2.71-2.80.29751380.18572636X-RAY DIFFRACTION98.06
2.8-2.90.32421470.1842651X-RAY DIFFRACTION98.38
2.9-3.010.26351370.18382657X-RAY DIFFRACTION98.45
3.01-3.150.26951430.18712672X-RAY DIFFRACTION98.98
3.15-3.310.29121440.182667X-RAY DIFFRACTION99.65
3.31-3.520.24521480.16082709X-RAY DIFFRACTION99.62
3.52-3.790.20621400.14272705X-RAY DIFFRACTION99.86
3.79-4.170.221540.13052683X-RAY DIFFRACTION99.3
4.17-4.780.18341470.12552688X-RAY DIFFRACTION99.54
4.78-6.010.20141420.13932703X-RAY DIFFRACTION99.44
6.01-28.70.20541550.17212717X-RAY DIFFRACTION99.21

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