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- PDB-3aro: Crystal Structure Analysis of Chitinase A from Vibrio harveyi wit... -

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Basic information

Entry
Database: PDB / ID: 3aro
TitleCrystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - apo structure
ComponentsChitinase A
KeywordsHYDROLASE / TIM BARREL / INHIBITOR COMPLEX / GLYCOSIDASE
Function / homology
Function and homology information


chitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / K319L-like, PKD domain / PKD domain / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / PKD domain / PKD domain superfamily / PKD/Chitinase domain ...Chitinase A N-terminal / Chitinase A, N-terminal domain / K319L-like, PKD domain / PKD domain / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsPantoom, S. / Vetter, I.R. / Prinz, H. / Suginta, W.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms
Authors: Pantoom, S. / Vetter, I.R. / Prinz, H. / Suginta, W.
#1: Journal: J.Struct.Biol. / Year: 2008
Title: Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism
Authors: Songsiriritthigul, C. / Pantoom, S. / Aguda, A.H. / Robinson, R.C. / Suginta, W.
History
DepositionDec 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9342
Polymers63,8421
Non-polymers921
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.820, 50.550, 93.260
Angle α, β, γ (deg.)90.000, 99.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitinase A


Mass: 63841.770 Da / Num. of mol.: 1 / Fragment: residues 22-597
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: LMG7890 / Gene: chiA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AMP1, chitinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 5.6
Details: 16%(W/V) PEG 4000, 21%(v/v) propanol, 0.1M Na-Acetate, pH 5.6, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2009 / Details: helios mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→19.822 Å / Num. obs: 28924 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.639 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.22-2.280.2630.1645.84514216020160.20893.3
2.28-2.340.1760.1317.65099209920860.16699.4
2.34-2.410.230.147.25079210520870.17899.1
2.41-2.490.2220.13984458196818630.17694.7
2.49-2.570.1780.1128.44720192819190.14299.5
2.57-2.660.1540.19.44728191819120.12699.7
2.66-2.760.1360.09110.84368177517680.11599.6
2.76-2.870.1730.10310.93706175015940.13391.1
2.87-30.1090.0713.14142168016640.08899
3-3.150.0830.05915.54001161216070.07499.7
3.15-3.320.0690.0518.23787153115230.06399.5
3.32-3.520.050.0421.63579144214360.0599.6
3.52-3.760.0440.03425.83354136113480.04399
3.76-4.060.040.03227.63176127912690.0499.2
4.06-4.450.0330.02829.82903117211590.03698.9
4.45-4.970.0340.02930.12648106610530.03698.8
4.97-5.740.0380.02927.423539539370.03798.3
5.74-7.030.0460.03623.919627967820.04598.2
7.03-9.950.0320.02632.315456376180.03397
9.950.0230.021416903702830.02876.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0093refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3b9a

3b9a


Resolution: 2.22→19.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.1834 / WRfactor Rwork: 0.1237 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8776 / SU B: 5.169 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2754 / SU Rfree: 0.2118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1447 5 %RANDOM
Rwork0.143 ---
obs0.1466 28924 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.13 Å2 / Biso mean: 14.1065 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.15 Å2
2---0.21 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.22→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4416 0 6 646 5068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224560
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9456208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93825.213211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30615696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8861513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213572
LS refinement shellResolution: 2.224→2.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 98 -
Rwork0.189 1824 -
all-1922 -
obs--92.99 %

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