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

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Basic information

Entry
Database: PDB / ID: 3ars
TitleCrystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - apo structure of mutant W275G
ComponentsChitinase A
KeywordsHYDROLASE / TIM BARREL / INHIBITOR COMPLEX / GLYCOSIDASE
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
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase A


Theoretical massNumber of molelcules
Total (without water)63,7131
Polymers63,7131
Non-polymers00
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.550, 83.580, 102.360
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
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 7, 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: 2.45→19.776 Å / Num. obs: 20987 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.745 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.52
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
2.45-2.510.690.434124156213400.48185.8
2.51-2.580.2630.2255.65204154115310.26899.4
2.58-2.660.3690.2454.95092149614900.29299.6
2.66-2.740.3130.2195.54889143314250.26199.4
2.74-2.830.3160.2216.34086140512950.26892.2
2.83-2.930.3150.26.64318137413050.2495
2.93-3.040.2030.1458.24516132113130.17399.4
3.04-3.160.1570.1219.64340126712660.14399.9
3.16-3.30.1350.09611.94205123412230.11399.1
3.3-3.460.1070.08413.94009116311580.199.6
3.46-3.650.0720.0618.53798110810990.07199.2
3.65-3.870.0670.05320.93651106510570.06299.2
3.87-4.140.0550.04424.9343810049930.05298.9
4.14-4.470.0530.04126.531849339190.04898.5
4.47-4.90.0550.0426.929668708550.04798.3
4.9-5.480.0540.04325.226407787630.0598.1
5.48-6.320.0780.05619.223667056880.06697.6
6.32-7.750.0630.0452320096105900.05496.7
7.75-10.950.0320.02835.215344754580.03396.4
10.950.0260.02142.16822902190.02575.5

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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: 2.45→19.776 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / WRfactor Rfree: 0.2066 / WRfactor Rwork: 0.1602 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8262 / SU B: 9.638 / SU ML: 0.211 / SU R Cruickshank DPI: 1.0719 / SU Rfree: 0.3171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 1050 5 %RANDOM
Rwork0.1978 ---
obs0.2008 20986 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.77 Å2 / Biso mean: 19.649 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 0 385 4729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224458
X-RAY DIFFRACTIONr_angle_refined_deg0.8651.9456063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95525.34206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98415682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.3471511
X-RAY DIFFRACTIONr_chiral_restr0.060.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213488
LS refinement shellResolution: 2.449→2.512 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 58 -
Rwork0.352 1149 -
all-1207 -
obs--84.46 %

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