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- PDB-9u3o: Crystal structure of Chi430 mutant E176A in the substrate complex -

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Basic information

Entry
Database: PDB / ID: 9u3o
TitleCrystal structure of Chi430 mutant E176A in the substrate complex
Componentschitinase
KeywordsHYDROLASE / Chitinase / complex
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: 1.35 Å
AuthorsQipeng, C. / Jinghan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32202987 China
CitationJournal: To Be Published
Title: Crystal structure of Chi430 mutant E173A in the substrate complex
Authors: Qipeng, C. / Jinghan, Z.
History
DepositionMar 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8844
Polymers46,0171
Non-polymers8673
Water3,783210
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)121.676, 49.858, 92.602
Angle α, β, γ (deg.)90.000, 125.616, 90.000
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 chitinase


Mass: 46017.387 Da / Num. of mol.: 1 / Mutation: E176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: HKB16_33210 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7Y0XG39, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate / PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.35→60.58 Å / Num. obs: 98938 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 6.58 Å2 / CC1/2: 0.974 / Net I/σ(I): 7.4
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7195 / CC1/2: 0.189
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→49.506 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.195 / SU B: 0.984 / SU ML: 0.039 / Average fsc free: 0.9619 / Average fsc work: 0.9674 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2033 4902 4.956 %
Rwork0.1842 94012 -
all0.185 --
obs-98914 99.769 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.787 Å2
Baniso -1Baniso -2Baniso -3
1--0.057 Å2-0 Å20.244 Å2
2---0.414 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.35→49.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 57 210 3505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123386
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163055
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.8094592
X-RAY DIFFRACTIONr_angle_other_deg0.691.7577068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.05856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53310540
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1310160
X-RAY DIFFRACTIONr_chiral_restr0.1040.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
X-RAY DIFFRACTIONr_nbd_refined0.2410.2705
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22858
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21702
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2173
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0560.210
X-RAY DIFFRACTIONr_nbd_other0.1490.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.210
X-RAY DIFFRACTIONr_mcbond_it1.2690.9431639
X-RAY DIFFRACTIONr_mcbond_other1.2690.9431639
X-RAY DIFFRACTIONr_mcangle_it1.971.6892047
X-RAY DIFFRACTIONr_mcangle_other1.9691.6912048
X-RAY DIFFRACTIONr_scbond_it2.4361.2231747
X-RAY DIFFRACTIONr_scbond_other2.4381.2231748
X-RAY DIFFRACTIONr_scangle_it3.8142.1152545
X-RAY DIFFRACTIONr_scangle_other3.8142.1142546
X-RAY DIFFRACTIONr_lrange_it4.67910.183929
X-RAY DIFFRACTIONr_lrange_other4.6649.8943898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.35-1.3850.3013590.29468270.29472510.9270.91699.10360.27
1.385-1.4230.2823520.26967300.26971280.8850.92599.35470.25
1.423-1.4640.2323360.22865500.22869170.9490.95499.55180.21
1.464-1.5090.2383430.21963400.2267010.9530.95699.73140.202
1.509-1.5590.2343270.19161980.19465420.9620.97399.74010.177
1.559-1.6130.2153350.18559440.18762850.9710.97299.90450.172
1.613-1.6740.2013050.17357250.17460340.9740.97799.93370.163
1.674-1.7420.1962850.17656030.17758920.9750.97799.93210.167
1.742-1.820.1922620.16453710.16656350.9760.9899.96450.161
1.82-1.9080.1942580.16250850.16353470.9770.98399.92520.164
1.908-2.0120.1842690.16348630.16451320.9780.9811000.168
2.012-2.1330.1862320.16146200.16248540.9760.98399.95880.172
2.133-2.280.1842250.16143440.16245690.9790.9831000.175
2.28-2.4630.1672040.15840360.15842410.9810.98599.97640.178
2.463-2.6970.1741650.17137530.17139190.980.98399.97450.198
2.697-3.0140.1951820.17333840.17435660.9750.981000.201
3.014-3.4780.2031620.17529840.17631460.9760.981000.211
3.478-4.2550.1661380.16125310.16126690.9850.9851000.208
4.255-5.9950.1941110.17919930.1821100.9810.98599.71560.24
5.995-49.5060.264520.25811310.25912030.9640.95198.33750.487

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