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- PDB-2xuc: Natural product-guided discovery of a fungal chitinase inhibitor -

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Basic information

Entry
Database: PDB / ID: 2xuc
TitleNatural product-guided discovery of a fungal chitinase inhibitor
ComponentsCHITINASE
KeywordsHYDROLASE / ASPERGILLOSIS
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / side of membrane / extracellular region / plasma membrane
Similarity search - Function
Chitinase Cts1-like / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 1-methyl-3-(N-methylcarbamimidoyl)urea / Endochitinase A1
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRush, C.L. / Schuttelkopf, A.W. / Hurtado-Guerrero, R. / Blair, D.E. / Ibrahim, A.F.M. / Desvergnes, S. / Eggleston, I.M. / van Aalten, D.M.F.
CitationJournal: Chem.Biol. / Year: 2010
Title: Natural Product-Guided Discovery of a Fungal Chitinase Inhibitor.
Authors: Rush, C.L. / Schuttelkopf, A.W. / Hurtado-Guerrero, R. / Blair, D.E. / Ibrahim, A.F.M. / Desvergnes, S. / Eggleston, I.M. / van Aalten, D.M.F.
History
DepositionOct 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 16, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / diffrn_source
Item: _audit_author.name / _citation_author.name / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHITINASE
B: CHITINASE
C: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,36214
Polymers102,2613
Non-polymers1,10211
Water3,189177
1
A: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4785
Polymers34,0871
Non-polymers3914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5736
Polymers34,0871
Non-polymers4865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3123
Polymers34,0871
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.039, 100.039, 111.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein CHITINASE / / CHITINASE A1


Mass: 34086.906 Da / Num. of mol.: 3 / Fragment: RESIDUES 29-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Plasmid: PPIC9 / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q873Y0, chitinase
#2: Chemical
ChemComp-XRG / 1-methyl-3-(N-methylcarbamimidoyl)urea


Mass: 130.148 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10N4O
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.86 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Type: ESRF / Wavelength: 0.931
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.3→25.01 Å / Num. obs: 55123 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4

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Processing

SoftwareName: REFMAC / Version: 5.5.0088 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→86.64 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.871 / SU B: 7.166 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27749 547 1 %RANDOM
Rwork0.23298 ---
obs0.23345 54479 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→86.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7094 0 67 177 7338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227286
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.9349924
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6285893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55124.957351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.647151025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8851515
X-RAY DIFFRACTIONr_chiral_restr0.1230.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215768
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.54482
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66727178
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.65232804
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9234.52746
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 36 -
Rwork0.27 3931 -
obs--97.76 %

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