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- PDB-7yv0: Structural Insight into a Metal-Dependent Mutase MtdL Revealing a... -

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Basic information

Entry
Database: PDB / ID: 7yv0
TitleStructural Insight into a Metal-Dependent Mutase MtdL Revealing an Arginine Residue Covalently Mediated Interconversion between Nucleotide-Based furanose and pyranose
ComponentsTransglycosylse
KeywordsBIOSYNTHETIC PROTEIN / Metal-Dependent Mutase
Function / homologySTELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / Transglycosylse
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å
AuthorsChi, C.B. / Ma, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2023
Title: Structural Insight into a Metal-Dependent Mutase Revealing an Arginine Residue-Covalently Mediated Interconversion between Nucleotide-Based Pyranose and Furanose.
Authors: Chi, C.B. / Xu, R. / Chen, Q.Q. / Zhang, X.H. / Shi, X.M. / Jin, H.W. / Yin, F. / Jia, H.L. / Zhang, L.R. / Yang, D.H. / Ju, J.H. / Li, Q.L. / Ma, M.
History
DepositionAug 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Transglycosylse
B: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4043
Polymers83,3082
Non-polymers961
Water2,234124
1
A: Transglycosylse
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7502
Polymers41,6541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area14800 Å2
MethodPISA
2
B: Transglycosylse


Theoretical massNumber of molelcules
Total (without water)41,6541
Polymers41,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.306, 98.273, 59.224
Angle α, β, γ (deg.)90.000, 97.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transglycosylse


Mass: 41653.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G8HX37
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 8000, 0.1 M HEPES 7.5

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.34→49.14 Å / Num. obs: 37896 / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.7
Reflection shellResolution: 2.34→2.42 Å / Rmerge(I) obs: 0.275 / Num. unique obs: 3686

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.34→31.191 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1997 5.28 %
Rwork0.201 35808 -
obs0.203 37805 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.85 Å2 / Biso mean: 42.7832 Å2 / Biso min: 22.07 Å2
Refinement stepCycle: final / Resolution: 2.34→31.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5802 0 0 124 5926
Biso mean---41.85 -
Num. residues----744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3401-2.39860.33141410.2941254996
2.3986-2.46340.34091410.2796251897
2.4634-2.53580.34071350.2733241993
2.5358-2.61760.34331430.2503258698
2.6176-2.71120.32661440.2364258298
2.7112-2.81960.29621440.23256798
2.8196-2.94790.26581460.2247260499
2.9479-3.10320.24461420.2206256898
3.1032-3.29740.25981390.2154248394
3.2974-3.55160.25261450.2012260199
3.5516-3.90850.20661460.1843261899
3.9085-4.47260.2021450.1684260599
4.4726-5.62960.20211410.1662253796

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