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

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Basic information

Entry
Database: PDB / ID: 3arr
TitleCrystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with PENTOXIFYLLINE
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-PNX / chitinase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 20, 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)64,3983
Polymers63,8421
Non-polymers5572
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.020, 85.340, 62.970
Angle α, β, γ (deg.)90.000, 112.900, 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-PNX / 3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE / PENTOXIFYLLINE


Mass: 278.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 8.5
Details: 1.1M Ammonium Sulfate, 0.1M Tris, pH 8.5, 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: 1.65→19.948 Å / Num. obs: 68396 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.031 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.34
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
1.65-1.690.5620.473.716179519150760.56497.8
1.69-1.740.490.4014.315777507049610.48397.9
1.74-1.790.3920.3295.115366490648250.39598.3
1.79-1.840.3160.2576.314918476446830.30998.3
1.84-1.910.2450.2017.514459462845480.24298.3
1.91-1.970.1980.1618.814036449444280.19498.5
1.97-2.050.1580.13710.113521432842560.16598.3
2.05-2.130.1250.10911.713004416540970.13298.4
2.13-2.220.1040.09313.112401398139140.11298.3
2.22-2.330.0890.08214.111853383737600.09998
2.33-2.460.0760.07415.411196361835410.08997.9
2.46-2.610.0690.06816.410619346133610.08297.1
2.61-2.790.0570.0617.79823320231100.07197.1
2.79-3.010.050.054199307304929420.06596.5
3.01-3.30.040.04921.38389277426490.05895.5
3.3-3.690.0320.04323.57511251523790.05194.6
3.69-4.260.0280.039256788223321110.04794.5
4.26-5.220.0260.03525.75703188817480.04292.6
5.22-7.380.0260.03425.14447146413450.0491.9
7.380.0220.02825.821188326620.03479.6

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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: 1.65→19.948 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.539 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 3420 5 %RANDOM
Rwork0.1434 ---
obs0.1456 68395 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.47 Å2 / Biso mean: 19.2401 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.34 Å2
2---0.33 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 40 697 5091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224594
X-RAY DIFFRACTIONr_angle_refined_deg2.3681.9536277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86825.333210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7715706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.931511
X-RAY DIFFRACTIONr_chiral_restr0.1890.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213608
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 246 -
Rwork0.184 4679 -
all-4925 -
obs--97.72 %

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