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- PDB-7vi8: Crystal structure of ChbG -

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Basic information

Entry
Database: PDB / ID: 7vi8
TitleCrystal structure of ChbG
ComponentsChitooligosaccharide deacetylase
KeywordsHYDROLASE / ChbG / Chitin catabolism / Chitin deacetylase / Chitobiose operon / Klebsiella pneumoniae
Function / homology
Function and homology information


chitin disaccharide deacetylase / chitin disaccharide deacetylase activity / diacetylchitobiose catabolic process / chitin catabolic process / polysaccharide catabolic process / metal ion binding / cytoplasm
Similarity search - Function
Chitooligosaccharide deacetylase ChbG-like, bacteria / Carbohydrate deacetylase YdjC-like / YdjC-like protein / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
ACETATE ION / Chitooligosaccharide deacetylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLee, S.Y. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Commun Biol / Year: 2022
Title: Crystal structure of ChbG from Klebsiella pneumoniae reveals the molecular basis of diacetylchitobiose deacetylation.
Authors: Lee, S.Y. / Pardhe, B.D. / Oh, T.J. / Park, H.H.
History
DepositionSep 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitooligosaccharide deacetylase
B: Chitooligosaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1095
Polymers55,9192
Non-polymers1903
Water6,990388
1
A: Chitooligosaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0843
Polymers27,9601
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-37 kcal/mol
Surface area10860 Å2
MethodPISA
2
B: Chitooligosaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0252
Polymers27,9601
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.230, 67.030, 146.400
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 Chitooligosaccharide deacetylase / COD / Chitin disaccharide deacetylase / Chitobiose deacetylase / Chitobiose-6P deacetylase / ...COD / Chitin disaccharide deacetylase / Chitobiose deacetylase / Chitobiose-6P deacetylase / Chitotriose deacetylase / Chitotriose-6P deacetylase


Mass: 27959.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Gene: chbG, KPN78578_12070, KPN_01235 / Production host: Escherichia coli (E. coli)
References: UniProt: A6T7U7, chitin disaccharide deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 15% (v/v) PEG 550 MME, 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.83→28.51 Å / Num. obs: 47465 / % possible obs: 99 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1074 / Net I/σ(I): 16.48
Reflection shellResolution: 1.83→1.895 Å / Rmerge(I) obs: 1.96 / Num. unique obs: 4668 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I5I

2i5i


Resolution: 1.83→28.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.148
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2569 2373 5 %
Rwork0.2203 45086 -
all0.222 --
obs-47459 99.003 %
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: 26.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.078 Å2-0 Å20 Å2
2--0.103 Å2-0 Å2
3----0.181 Å2
Refinement stepCycle: LAST / Resolution: 1.83→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 6 388 4279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133968
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173683
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.635380
X-RAY DIFFRACTIONr_angle_other_deg2.3211.5728442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31521.339224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27815631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1441533
X-RAY DIFFRACTIONr_chiral_restr0.1010.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024583
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02939
X-RAY DIFFRACTIONr_nbd_refined0.2180.2866
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.23559
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22033
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1460.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.210
X-RAY DIFFRACTIONr_nbd_other0.1990.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.223
X-RAY DIFFRACTIONr_mcbond_it3.192.6832015
X-RAY DIFFRACTIONr_mcbond_other3.1782.6812013
X-RAY DIFFRACTIONr_mcangle_it3.6444.0022514
X-RAY DIFFRACTIONr_mcangle_other3.6454.0042515
X-RAY DIFFRACTIONr_scbond_it4.3522.9471953
X-RAY DIFFRACTIONr_scbond_other4.3512.9471954
X-RAY DIFFRACTIONr_scangle_it5.3314.3012866
X-RAY DIFFRACTIONr_scangle_other5.334.3022867
X-RAY DIFFRACTIONr_lrange_it5.56133.0244639
X-RAY DIFFRACTIONr_lrange_other5.56233.0294640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.8770.3641750.3133318X-RAY DIFFRACTION99.7145
1.877-1.9290.3331690.2933209X-RAY DIFFRACTION99.4993
1.929-1.9850.3531640.2853125X-RAY DIFFRACTION99.6667
1.985-2.0460.3351600.2733044X-RAY DIFFRACTION99.3488
2.046-2.1130.2951530.2712924X-RAY DIFFRACTION98.9071
2.113-2.1870.2871500.2622845X-RAY DIFFRACTION98.9428
2.187-2.2690.321460.2562766X-RAY DIFFRACTION98.8124
2.269-2.3620.2641380.2562629X-RAY DIFFRACTION98.4347
2.362-2.4670.2891330.2532529X-RAY DIFFRACTION97.9757
2.467-2.5870.2491280.2462422X-RAY DIFFRACTION98.228
2.587-2.7270.2751210.2372309X-RAY DIFFRACTION98.6201
2.727-2.8920.2831160.2312204X-RAY DIFFRACTION98.5556
2.892-3.0910.2471080.2262055X-RAY DIFFRACTION98.3629
3.091-3.3390.2651030.2181946X-RAY DIFFRACTION99.0812
3.339-3.6570.25950.21798X-RAY DIFFRACTION99.1619
3.657-4.0870.215860.1781646X-RAY DIFFRACTION99.3689
4.087-4.7170.189780.1641469X-RAY DIFFRACTION99.8064
4.717-5.7710.22660.1751259X-RAY DIFFRACTION100
5.771-8.1360.204530.191002X-RAY DIFFRACTION100
8.136-28.510.199310.175587X-RAY DIFFRACTION96.8652

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