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- PDB-7xh0: crystal structure of Csn-PD from Paenibacillus dendritiformis -

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Basic information

Entry
Database: PDB / ID: 7xh0
Titlecrystal structure of Csn-PD from Paenibacillus dendritiformis
ComponentsChitosanase
KeywordsHYDROLASE / chitosanase GH46 family
Function / homology
Function and homology information


chitosanase / chitosanase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitosanases families 46 and 80 active sites signature. / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily
Similarity search - Domain/homology
CITRATE ANION / Chitosanase
Similarity search - Component
Biological speciesPaenibacillus dendritiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSun, H.H. / Cheng, Y.M. / Cao, R. / Liu, Q. / Zhao, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31801574 China
CitationJournal: To Be Published
Title: crystal structure of Csn-PD from Paenibacillus dendritiformis
Authors: Sun, H.H. / Cheng, Y.M. / Cao, R. / Liu, Q. / Zhao, L.
History
DepositionApr 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6093
Polymers34,3581
Non-polymers2512
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40 Å2
ΔGint0 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.510, 73.138, 99.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chitosanase


Mass: 34357.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus dendritiformis (bacteria)
Gene: DOE73_06680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2W4GVN6, chitosanase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.82 Å3/Da / Density % sol: 32.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Citric acid pH3.5, 25% PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18071 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18071 Å / Relative weight: 1
ReflectionResolution: 1.68→44.72 Å / Num. obs: 28796 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.7
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 0.446 / Num. unique obs: 1417

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d05

2d05


Resolution: 1.68→44.72 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.993 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1951 1455 5.058 %
Rwork0.1497 27311 -
all0.152 --
obs-28766 99.244 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.494 Å2
Baniso -1Baniso -2Baniso -3
1-2.846 Å2-0 Å20 Å2
2---1.079 Å2-0 Å2
3----1.767 Å2
Refinement stepCycle: LAST / Resolution: 1.68→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 17 238 2285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132110
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161958
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.6462850
X-RAY DIFFRACTIONr_angle_other_deg1.5571.5984529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46324.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94515375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.218159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_nbd_refined0.220.2486
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21932
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21109
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1160.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.219
X-RAY DIFFRACTIONr_nbd_other0.1840.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.220
X-RAY DIFFRACTIONr_mcbond_it1.6561.9661039
X-RAY DIFFRACTIONr_mcbond_other1.631.9641038
X-RAY DIFFRACTIONr_mcangle_it2.2692.9431299
X-RAY DIFFRACTIONr_mcangle_other2.272.9451300
X-RAY DIFFRACTIONr_scbond_it3.0222.3141070
X-RAY DIFFRACTIONr_scbond_other3.0212.3161071
X-RAY DIFFRACTIONr_scangle_it4.63.3041547
X-RAY DIFFRACTIONr_scangle_other4.5983.3061548
X-RAY DIFFRACTIONr_lrange_it5.57624.7752629
X-RAY DIFFRACTIONr_lrange_other5.49624.2622575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.7240.249950.2061965X-RAY DIFFRACTION97.5379
1.724-1.7710.256890.21939X-RAY DIFFRACTION98.2558
1.771-1.8220.192900.1741886X-RAY DIFFRACTION98.5536
1.822-1.8780.2281040.1751807X-RAY DIFFRACTION98.7597
1.878-1.940.2641010.1661794X-RAY DIFFRACTION99.2147
1.94-2.0080.1811010.1541706X-RAY DIFFRACTION99.4496
2.008-2.0830.218840.1541683X-RAY DIFFRACTION99.2697
2.083-2.1680.18970.1451591X-RAY DIFFRACTION99.3526
2.168-2.2640.1751010.1411527X-RAY DIFFRACTION99.7549
2.264-2.3750.177710.1331501X-RAY DIFFRACTION99.5567
2.375-2.5030.195660.1361425X-RAY DIFFRACTION99.7992
2.503-2.6540.216560.1391361X-RAY DIFFRACTION99.8591
2.654-2.8370.204530.1361269X-RAY DIFFRACTION99.9244
2.837-3.0630.201690.1491177X-RAY DIFFRACTION99.9198
3.063-3.3540.217630.1561100X-RAY DIFFRACTION99.9141
3.354-3.7480.188760.144969X-RAY DIFFRACTION99.809
3.748-4.3240.134560.122878X-RAY DIFFRACTION99.5736
4.324-5.2860.187370.145764X-RAY DIFFRACTION100
5.286-7.4340.241240.187608X-RAY DIFFRACTION99.842
7.434-44.720.2220.158361X-RAY DIFFRACTION99.2228

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