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- PDB-8qhf: Corynebacterium glutamicum mycoloyltransferase C acyl-enzyme inte... -

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Basic information

Entry
Database: PDB / ID: 8qhf
TitleCorynebacterium glutamicum mycoloyltransferase C acyl-enzyme intermediate
ComponentsCmt1
KeywordsTRANSFERASE / ALPHA / BETA HYDROLASE / MYCOLOYLTRANSFERASE / TREHALOSE O- 2 MYCOLYLTRANSFERASE / EXTERNAL MEMBRANE / TMM analogs
Function / homology: / Esterase-like / Putative esterase / acyltransferase activity, transferring groups other than amino-acyl groups / Alpha/Beta hydrolase fold / metal ion binding / trehalose / : / Cmt1
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLi de la Sierra-Gallay, I. / Lesur, E.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Synthetic mycolates derivatives to decipher protein mycoloylation, a unique post-translational modification in bacteria.
Authors: Lesur, E. / Zhang, Y. / Dautin, N. / Dietrich, C. / Li de la Sierra-Gallay, I. / Augusto, L.A. / Rollando, P. / Lazar, N. / Urban, D. / Doisneau, G. / Constantinesco-Becker, F. / Van ...Authors: Lesur, E. / Zhang, Y. / Dautin, N. / Dietrich, C. / Li de la Sierra-Gallay, I. / Augusto, L.A. / Rollando, P. / Lazar, N. / Urban, D. / Doisneau, G. / Constantinesco-Becker, F. / Van Tilbeurgh, H. / Guianvarc'h, D. / Bourdreux, Y. / Bayan, N.
History
DepositionSep 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cmt1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3348
Polymers39,5371
Non-polymers7977
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.120, 168.120, 168.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cmt1


Mass: 39537.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cmt1 / Production host: Corynebacterium glutamicum (bacteria) / References: UniProt: Q8NTG4
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 37 molecules

#3: Chemical ChemComp-VBL / (2~{S},3~{R})-2-pentyloctane-1,3-diol


Mass: 216.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: Ammonium sulfate, Sodium chloride, Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 2.688→48.53 Å / Num. obs: 11045 / % possible obs: 99.6 % / Redundancy: 9.7 % / CC1/2: 0.997 / Rrim(I) all: 0.198 / Net I/σ(I): 12.21
Reflection shellResolution: 2.69→2.85 Å / Num. unique obs: 1723 / CC1/2: 0.349 / Rrim(I) all: 2.449

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→48.53 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 1.321 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.148 / SU Rfree Blow DPI: 0.354 / SU Rfree Cruickshank DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 553 5.01 %RANDOM
Rwork0.2532 ---
obs0.2545 11045 99.7 %-
Displacement parametersBiso mean: 85.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.69→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 47 31 2590
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072620HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893571HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d866SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes443HARMONIC5
X-RAY DIFFRACTIONt_it2620HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion14.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion341SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1995SEMIHARMONIC4
LS refinement shellResolution: 2.69→2.73 Å / Total num. of bins used: 28
RfactorNum. reflection% reflection
Rfree0.5176 -5.12 %
Rwork0.4002 389 -
all0.4061 410 -
obs--92.47 %

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