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- PDB-7fd6: Crystal structure of SmChiA in complex with 6a -

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Basic information

Entry
Database: PDB / ID: 7fd6
TitleCrystal structure of SmChiA in complex with 6a
ComponentsChitinase A
KeywordsHYDROLASE / SmChiA / Inhibitor / chitinase
Function / homology
Function and homology information


chitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-4QU / Chitinase A
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsXi, J. / Qing, Y.
CitationJournal: To Be Published
Title: Discovery of Conformation Constrained Tetracyclic Compounds as potent Chitinase OfChi-h inhibitor with novel binding mode
Authors: Pengtao, Y. / Xi, J.
History
DepositionJul 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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)60,1272
Polymers59,7571
Non-polymers3701
Water13,511750
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21200 Å2
Unit cell
Length a, b, c (Å)132.525, 202.186, 59.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Chitinase A


Mass: 59756.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiA, PWN146_04604 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C3HLG1, chitinase
#2: Chemical ChemComp-4QU / 11-methyl-3-(pyridin-3-ylmethyl)-4H-pyrimido[5'',4'':5',6']pyrido[2',3':4,5]pyrimido[1,2-b]pyridine-4,6(3H)-dione


Mass: 370.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.75 M sodium citrate, 20% (v/v) methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.786→34.92 Å / Num. obs: 74412 / % possible obs: 97.82 % / Redundancy: 8.6 % / Biso Wilson estimate: 18.56 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.76
Reflection shellResolution: 1.786→1.85 Å / Num. unique obs: 6152 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EDQ

1edq


Resolution: 1.79→34.92 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0157 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1902 2000 2.69 %
Rwork0.1663 72400 -
obs0.1669 74400 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.01 Å2
Refinement stepCycle: LAST / Resolution: 1.79→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 28 750 4901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344258
X-RAY DIFFRACTIONf_angle_d0.60055783
X-RAY DIFFRACTIONf_chiral_restr0.0482611
X-RAY DIFFRACTIONf_plane_restr0.0037751
X-RAY DIFFRACTIONf_dihedral_angle_d11.08732464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.25881090.23083949X-RAY DIFFRACTION75.64
1.83-1.880.24561400.22315066X-RAY DIFFRACTION97.02
1.88-1.940.21341420.2115168X-RAY DIFFRACTION98.64
1.94-20.22891440.19535201X-RAY DIFFRACTION99.28
2-2.070.20211450.1915241X-RAY DIFFRACTION99.74
2.07-2.150.21591450.18165218X-RAY DIFFRACTION99.93
2.15-2.250.22931440.17845258X-RAY DIFFRACTION99.87
2.25-2.370.20791460.17595266X-RAY DIFFRACTION99.89
2.37-2.520.19521440.17515246X-RAY DIFFRACTION99.96
2.52-2.710.18021470.17535286X-RAY DIFFRACTION99.94
2.71-2.980.22911460.17185294X-RAY DIFFRACTION99.87
2.98-3.420.16241460.15935308X-RAY DIFFRACTION99.8
3.42-4.30.14871480.13425362X-RAY DIFFRACTION99.64
4.3-34.920.1711540.14065537X-RAY DIFFRACTION99.49

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