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- PDB-9iuh: Crystal structure of Chitinase from Vibrio parahaemolyticus at pH6.5 -

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Basic information

Entry
Database: PDB / ID: 9iuh
TitleCrystal structure of Chitinase from Vibrio parahaemolyticus at pH6.5
ComponentsGlycoside hydrolase family 18 protein
KeywordsHYDROLASE / Chitinase / GH18 family
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 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycoside hydrolase family 18 protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCheng, Q. / Zhang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32202987 China
CitationJournal: To Be Published
Title: Crystal structure of Chitinase from Vibrio parahaemolyticus at pH6.5
Authors: Cheng, Q. / Zhang, J.
History
DepositionJul 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 18 protein


Theoretical massNumber of molelcules
Total (without water)46,0751
Polymers46,0751
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.060, 50.420, 95.330
Angle α, β, γ (deg.)90.00, 126.53, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Glycoside hydrolase family 18 protein


Mass: 46075.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: HKB16_33210
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A7Y0XG39
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% v/v PEG 500* MME, 10 % w/v PEG 20000, 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Imidazole, 0.1M MES monohydrate (acid), pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.96183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96183 Å / Relative weight: 1
ReflectionResolution: 1.7→25.34 Å / Num. obs: 51910 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Net I/σ(I): 15.6
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 1.026 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3826 / CC1/2: 0.658 / Rpim(I) all: 0.469

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.409 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22891 2594 5 %RANDOM
Rwork0.19585 ---
obs0.1975 49312 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20.5 Å2
2---0.65 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.7→25.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 0 225 3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123343
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163017
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.6584533
X-RAY DIFFRACTIONr_angle_other_deg0.5491.5846977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.14956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77410544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1442.3811643
X-RAY DIFFRACTIONr_mcbond_other2.1382.3811643
X-RAY DIFFRACTIONr_mcangle_it2.9054.2782052
X-RAY DIFFRACTIONr_mcangle_other2.9044.282053
X-RAY DIFFRACTIONr_scbond_it3.3542.7211700
X-RAY DIFFRACTIONr_scbond_other3.3532.7231701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9474.8522482
X-RAY DIFFRACTIONr_long_range_B_refined5.6823.853775
X-RAY DIFFRACTIONr_long_range_B_other5.64223.533742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 197 -
Rwork0.37 3606 -
obs--99.92 %

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