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

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Basic information

Entry
Database: PDB / ID: 3arv
TitleCrystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with Sanguinarine
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
Chem-SAU / chitinase
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 1.4Nov 6, 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)64,7836
Polymers63,8421
Non-polymers9415
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.230, 50.820, 93.390
Angle α, β, γ (deg.)90.000, 99.490, 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-SAU / 13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium / Sanguinarine


Mass: 332.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14NO4
#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.: 847 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSAU A 607 IS WEAK BINDING SITE

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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: 2.39 Å3/Da / Density % sol: 48.57 %
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→39.873 Å / Num. obs: 95965 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.398 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.62
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
1.5-1.540.1750.1538.120731713767620.18494.7
1.54-1.580.1440.1319.221811694469260.15799.7
1.58-1.630.130.11710.121315676767570.1499.9
1.63-1.680.1060.10111.320682657365530.12199.7
1.68-1.730.0920.08712.520060637063530.10599.7
1.73-1.790.0780.07613.519549617361650.09199.9
1.79-1.860.0720.06814.618664594559180.08299.5
1.86-1.940.0570.0616.117985574357000.07299.3
1.94-2.020.050.05417.517289550454700.06599.4
2.02-2.120.0440.0518.716434530652450.0698.9
2.12-2.230.040.0462015501498349430.05599.2
2.23-2.370.0390.0562116038474646910.06698.8
2.37-2.530.0360.062216878446444250.06999.1
2.53-2.740.0350.06623.117840414841110.07599.1
2.74-30.0350.07124.620250384938150.07899.1
3-3.350.0330.06926.420561347934500.07699.2
3.35-3.870.0320.06226.516872308630440.06998.6
3.87-4.740.030.05425.913135261325590.06197.9
4.74-6.70.0290.05326.410481205019890.0697
6.70.0290.04823.94907116310890.05693.6

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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: 1.5→39.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1911 / WRfactor Rwork: 0.1547 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9101 / SU B: 0.978 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0621 / SU Rfree: 0.0665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 4799 5 %RANDOM
Rwork0.1444 ---
obs0.146 95964 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: 94.92 Å2 / Biso mean: 15.2226 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.09 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 68 847 5320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224822
X-RAY DIFFRACTIONr_angle_refined_deg2.4371.9646624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82225.3217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10515738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.631512
X-RAY DIFFRACTIONr_chiral_restr0.1610.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213798
X-RAY DIFFRACTIONr_mcbond_it1.4941.52953
X-RAY DIFFRACTIONr_mcangle_it2.50424778
X-RAY DIFFRACTIONr_scbond_it3.39331869
X-RAY DIFFRACTIONr_scangle_it5.1424.51817
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 338 -
Rwork0.165 6415 -
all-6753 -
obs--100 %

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