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

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Basic information

Entry
Database: PDB / ID: 3art
TitleCrystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant complex structure with DEQUALINIUM
ComponentsChitinase A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TIM BARREL / INHIBITOR COMPLEX / GLYCOSIDASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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
DEQUALINIUM / chitinase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 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 1.4Oct 23, 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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1755
Polymers63,7131
Non-polymers1,4624
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.600, 84.150, 102.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase A


Mass: 63712.621 Da / Num. of mol.: 1 / Fragment: residues 22-597 / Mutation: W275G
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-DEQ / DEQUALINIUM / DEQUADIN


Mass: 456.665 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C30H40N4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsDEQ A 606 AND 608 ARE WEAK BINDING SITES

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 5.5
Details: 26%(w/v) PEG 4000, 0.2M Ammonium Acetate, 0.1M Sodium Acetate, pH 5.5, 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 8, 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: 2.23→19.936 Å / Num. obs: 28235 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.618 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.64
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
2.23-2.290.4530.394.67036210017710.44784.3
2.29-2.350.2310.2566.88979203520320.28999.9
2.35-2.420.2270.2427.28739196919680.27499.9
2.42-2.490.2170.217.98597193119290.23899.9
2.49-2.580.1870.1878.98264186518610.21299.8
2.58-2.670.1620.179.88161182718240.19299.8
2.67-2.770.1570.14411.27826175117500.16399.9
2.77-2.880.1330.12312.77468167816720.13999.6
2.88-3.010.1110.10913.97326164216400.12399.9
3.01-3.160.0970.09116.26899154815460.10399.9
3.16-3.330.0720.0719.66509147214720.08100
3.33-3.530.0550.05624.36268141214090.06499.8
3.53-3.770.0410.04329.75834131913180.04999.9
3.77-4.070.0350.03833.35476123912380.04399.9
4.07-4.460.0310.034365009115711530.03999.7
4.46-4.990.0320.03438.34460102810250.03999.7
4.99-5.760.0350.03535.840639359270.0499.1
5.76-7.060.0420.0430.734428087910.04597.9
7.06-9.980.0240.02943.526056316080.03396.4
9.980.020.02151.112253813010.02579

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3b9a

3b9a


Resolution: 2.23→19.936 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.1966 / WRfactor Rwork: 0.1409 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8601 / SU B: 5.539 / SU ML: 0.139 / SU R Cruickshank DPI: 0.3126 / SU Rfree: 0.2238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1412 5 %RANDOM
Rwork0.1616 ---
obs0.1649 28235 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.47 Å2 / Biso mean: 16.7136 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.23→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4359 0 108 446 4913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224681
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9696386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07925.381210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65815709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6931511
X-RAY DIFFRACTIONr_chiral_restr0.1280.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213660
X-RAY DIFFRACTIONr_mcbond_it0.9521.52852
X-RAY DIFFRACTIONr_mcangle_it1.67124581
X-RAY DIFFRACTIONr_scbond_it2.91731829
X-RAY DIFFRACTIONr_scangle_it4.3334.51792
LS refinement shellResolution: 2.231→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 87 -
Rwork0.284 1654 -
all-1741 -
obs--100 %

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