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- PDB-6sx4: Structure of C. glutamicum mycoloyltransferase A -

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Basic information

Entry
Database: PDB / ID: 6sx4
TitleStructure of C. glutamicum mycoloyltransferase A
ComponentsProtein PS1
KeywordsTRANSFERASE / Mycoloyltransferase / Mycolic acid / cell wall
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / extracellular region
Similarity search - Function
LGFP / LGFP repeat / : / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / Protein PS1
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.796 Å
AuthorsLi de la Sierra-Gallay, I. / Van tilbeurgh, H. / Bayan, N.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INBS-05 France
CitationJournal: Mol.Microbiol. / Year: 2020
Title: The C-terminal domain of Corynebacterium glutamicum mycoloyltransferase A is composed of five repeated motifs involved in cell wall binding and stability.
Authors: Dietrich, C. / Li de la Sierra-Gallay, I. / Masi, M. / Girard, E. / Dautin, N. / Constantinesco-Becker, F. / Tropis, M. / Daffe, M. / van Tilbeurgh, H. / Bayan, N.
History
DepositionSep 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Protein PS1
BBB: Protein PS1
CCC: Protein PS1
DDD: Protein PS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,51429
Polymers270,0384
Non-polymers1,47625
Water3,765209
1
AAA: Protein PS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9238
Polymers67,5101
Non-polymers4137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Protein PS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8056
Polymers67,5101
Non-polymers2955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Protein PS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8647
Polymers67,5101
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Protein PS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9238
Polymers67,5101
Non-polymers4137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.150, 170.480, 241.850
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
Protein PS1


Mass: 67509.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: csp1, cop1, Cgl2875, cg3182 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P0C1D6
#2: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 25% PEG3350, 0.2M Ammonium Acetate, 0.05M Bis-Tris buffer, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2011
RadiationMonochromator: silicon Si crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.796→48.6 Å / Num. obs: 128339 / % possible obs: 99.7 % / Redundancy: 4.29 % / CC1/2: 0.989 / Rrim(I) all: 0.277 / Net I/σ(I): 5.12
Reflection shellResolution: 2.796→2.96 Å / Num. unique obs: 20491 / CC1/2: 0.62 / Rrim(I) all: 1.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.796→48.572 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R Free: 0.4
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2624 3444 5.097 %
Rwork0.2419 --
all0.243 --
obs-67565 99.711 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.744 Å2
Baniso -1Baniso -2Baniso -3
1-8.713 Å20 Å20 Å2
2---4.358 Å20 Å2
3----4.355 Å2
Refinement stepCycle: LAST / Resolution: 2.796→48.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18056 0 100 209 18365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01318607
X-RAY DIFFRACTIONr_bond_other_d0.0360.01716258
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.64225288
X-RAY DIFFRACTIONr_angle_other_deg2.3881.5737713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6552349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82522.963972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85152628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6711596
X-RAY DIFFRACTIONr_chiral_restr0.0550.22368
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221539
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024105
X-RAY DIFFRACTIONr_nbd_refined0.2040.23908
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2350.215760
X-RAY DIFFRACTIONr_nbtor_refined0.1680.28811
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.28042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2403
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1740.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.225
X-RAY DIFFRACTIONr_nbd_other0.2290.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.24
X-RAY DIFFRACTIONr_mcbond_it2.8225.5419445
X-RAY DIFFRACTIONr_mcbond_other2.825.5419437
X-RAY DIFFRACTIONr_mcangle_it4.6248.30711761
X-RAY DIFFRACTIONr_mcangle_other4.6248.30811762
X-RAY DIFFRACTIONr_scbond_it2.6185.6719162
X-RAY DIFFRACTIONr_scbond_other2.6185.6719163
X-RAY DIFFRACTIONr_scangle_it4.4428.41113527
X-RAY DIFFRACTIONr_scangle_other4.4428.41113528
X-RAY DIFFRACTIONr_lrange_it7.29662.68920460
X-RAY DIFFRACTIONr_lrange_other7.29662.69620457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.796-2.8680.4352470.4214524X-RAY DIFFRACTION97.3078
2.868-2.9460.3742370.3914615X-RAY DIFFRACTION99.9176

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