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

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Basic information

Entry
Database: PDB / ID: 3arp
TitleCrystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 30, 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)64,5755
Polymers63,8421
Non-polymers7334
Water15,925884
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.240, 50.970, 93.310
Angle α, β, γ (deg.)90.00, 99.53, 90.00
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-DEQ / DEQUALINIUM / DEQUADIN


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


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


Mass: 18.015 Da / Num. of mol.: 884 / 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: 48.68 %
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: 0.97941 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2009
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.55→19.976 Å / Num. obs: 85182 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.302 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.46
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
1.55-1.590.4810.322315271654456940.39487
1.59-1.630.3840.2743.816309628356960.3390.7
1.63-1.680.30.2254.716955610257130.2793.6
1.68-1.730.2370.1845.817290595356570.2295
1.73-1.790.1970.1547.117645577055600.18496.4
1.79-1.850.1550.1268.918061560254600.1597.5
1.85-1.920.120.10511.118148542853080.12497.8
1.92-20.0880.08114.518116518551260.09698.9
2-2.090.0730.0716.918106499049550.08299.3
2.09-2.190.0620.062017877478747620.0799.5
2.19-2.310.050.05123.217530456245430.0699.6
2.31-2.450.0420.04725.916942428642700.05499.6
2.45-2.620.0370.04228.416288404140310.04999.8
2.62-2.830.0310.03831.915567380837980.04399.7
2.83-3.10.0260.03335.714148345734450.03899.7
3.1-3.470.0210.034112908317631630.03499.6
3.47-40.0180.0264511221278627720.0399.5
4-4.90.0150.024479715237223630.02799.6
4.9-6.930.0150.02246.27649186418630.02599.9
6.930.0130.01947.53967106010030.02294.6

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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: 1.55→19.976 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1799 / WRfactor Rwork: 0.1434 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8994 / SU B: 1.265 / SU ML: 0.047 / SU R Cruickshank DPI: 0.071 / SU Rfree: 0.0766 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.187 4259 5 %RANDOM
Rwork0.1463 ---
obs0.1483 85180 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: 62.13 Å2 / Biso mean: 16.8028 Å2 / Biso min: 2.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.42 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4397 0 52 884 5333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224753
X-RAY DIFFRACTIONr_angle_refined_deg2.3911.9586511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38725.302215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49115728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1711512
X-RAY DIFFRACTIONr_chiral_restr0.1720.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213736
X-RAY DIFFRACTIONr_mcbond_it1.4681.52930
X-RAY DIFFRACTIONr_mcangle_it2.33724734
X-RAY DIFFRACTIONr_scbond_it3.33631823
X-RAY DIFFRACTIONr_scangle_it4.8784.51752
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 282 -
Rwork0.195 5375 -
all-5657 -
obs--100 %

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