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- PDB-8jqe: Structure of CmCBDA in complex with Mn2+ and glycerol -

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Basic information

Entry
Database: PDB / ID: 8jqe
TitleStructure of CmCBDA in complex with Mn2+ and glycerol
ComponentsYdjC family protein
KeywordsHYDROLASE / CmCBDA / N-acetylglucosamine deacetylase / mentalloenzyme / enzyme engineering
Function / homologyCarbohydrate deacetylase YdjC-like / YdjC-like protein / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / metal ion binding / : / PHOSPHATE ION / YdjC family protein
Function and homology information
Biological speciesCyclobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsLi, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structural Insights into the Catalytic Activity of Cyclobacterium marinum N -Acetylglucosamine Deacetylase.
Authors: Hu, S. / Xu, L. / Xie, C. / Hong, J.
History
DepositionJun 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YdjC family protein
B: YdjC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1528
Polymers70,6682
Non-polymers4846
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.617, 60.270, 87.444
Angle α, β, γ (deg.)90.00, 111.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YdjC family protein


Mass: 35334.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyclobacterium marinum (bacteria) / Gene: Cycma_4778 / Production host: Escherichia coli (E. coli) / References: UniProt: G0J5L4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.04M potassium dihydrogen phosphate, 16% PEG 8000, 20% Glycerol, 10mM MnCl2, 10 mM GlcNAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 28934 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 32.62 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.49
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.522 / Num. unique obs: 1414

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→34.99 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1401 4.85 %
Rwork0.1595 --
obs0.1621 28912 99.18 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 24 124 4887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094867
X-RAY DIFFRACTIONf_angle_d0.9016572
X-RAY DIFFRACTIONf_dihedral_angle_d5.939625
X-RAY DIFFRACTIONf_chiral_restr0.05701
X-RAY DIFFRACTIONf_plane_restr0.007852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.390.24171290.1842602X-RAY DIFFRACTION95
2.39-2.490.23261420.1752726X-RAY DIFFRACTION99
2.49-2.60.24481330.16062748X-RAY DIFFRACTION100
2.6-2.730.22691450.16062756X-RAY DIFFRACTION100
2.74-2.910.24731600.15832729X-RAY DIFFRACTION100
2.91-3.130.18311510.15462749X-RAY DIFFRACTION100
3.13-3.450.21891510.14542747X-RAY DIFFRACTION100
3.45-3.940.21861350.14742796X-RAY DIFFRACTION100
3.94-4.970.1831210.14882798X-RAY DIFFRACTION100
4.97-34.990.211340.18152860X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.57230.2150.71121.78180.70562.44750.1028-0.726-0.07650.21150.0194-0.3650.0740.0968-0.09190.2443-0.0289-0.07010.46530.01230.366417.95216.88272.1091
21.80280.11140.11442.03420.11581.2617-0.02960.1203-0.04-0.1958-0.0003-0.108-0.01330.10190.03440.1816-0.01720.02090.14180.020.2071-2.9110.268738.9267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 296)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 289)

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