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

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Basic information

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


chitinase activity / 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 / Carbohydrate-binding module family 5/12 / PKD domain / 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 / Carbohydrate-binding module family 5/12 / PKD domain / 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 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Roll / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CTI / Chitinase A
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 16, 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)64,3744
Polymers63,8421
Non-polymers5333
Water16,682926
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.010, 50.780, 93.290
Angle α, β, γ (deg.)90.000, 99.590, 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-CTI / 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium / chelerythrine


Mass: 348.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18NO4 / Comment: inhibitor, alkaloid*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2009
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.5→44.455 Å / Num. obs: 92812 / % possible obs: 96 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.417 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.54
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
1.5-1.540.4540.2913.712312712357860.37881.2
1.54-1.580.3710.2584.717038691366640.32696.4
1.58-1.620.3180.2285.819230674166780.28499.1
1.62-1.670.250.1876.918895654764950.23299.2
1.67-1.730.2020.1568.318626633562910.19399.3
1.73-1.790.1570.1289.818327617061230.15799.2
1.79-1.860.1290.10711.517675592658570.13298.8
1.86-1.930.0990.08613.817148572556390.10598.5
1.93-2.020.0760.0711616405547353460.08797.7
2.02-2.120.0650.06317.915819527551210.07797.1
2.12-2.230.0550.05419.514834498748170.06696.6
2.23-2.370.0480.0520.814035471645450.0696.4
2.37-2.530.0440.04721.913230444342720.05796.2
2.53-2.730.0390.04323.212300414739680.05195.7
2.73-30.0370.04124.511362383236820.0596.1
3-3.350.0320.03826.310200346632960.04695.1
3.35-3.870.0280.03627.89018307929110.04394.5
3.87-4.740.0260.033287405259824450.0494.1
4.74-6.70.0250.03227.75826204819150.03993.5
6.70.0260.03226.6266611599610.03982.9

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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: 1.5→44.455 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1948 / WRfactor Rwork: 0.1566 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9006 / SU B: 1.172 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0682 / SU Rfree: 0.0736 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 4641 5 %RANDOM
Rwork0.1526 ---
obs0.1545 92811 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.85 Å2 / Biso mean: 17.655 Å2 / Biso min: 3.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.19 Å2
2--0.08 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 38 926 5369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224762
X-RAY DIFFRACTIONr_angle_refined_deg2.4271.9566530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86725.3217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22415730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2541512
X-RAY DIFFRACTIONr_chiral_restr0.1610.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213755
LS refinement shellResolution: 1.498→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 286 -
Rwork0.223 5432 -
all-5718 -
obs--81.18 %

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