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- PDB-8j2n: Exopolysaccharide phosphotransferase CpsY in Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 8j2n
TitleExopolysaccharide phosphotransferase CpsY in Mycobacterium tuberculosis
ComponentsExopolysaccharide phosphotransferase CpsY
KeywordsTRANSFERASE / Phosphotransferase CpsY / Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) / Gene name Rv0806c / Taxonomic 83332 NCBI / P9WGD1
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups / polysaccharide biosynthetic process / peptidoglycan-based cell wall
Similarity search - Function
Stealth protein CR2, conserved region 2 / Stealth protein CR4, conserved region 4 / Stealth protein CR3, conserved region 3 / Stealth protein CR1, conserved region 1 / : / Stealth protein CR2, conserved region 2 / Stealth protein CR1, conserved region 1 / Stealth protein CR3, conserved region 3 / Stealth protein CR4, conserved region 4
Similarity search - Domain/homology
Exopolysaccharide phosphotransferase CpsY
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsLiu, D.F.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentNone China
CitationJournal: To Be Published
Title: Exopolysaccharide phosphotransferase CpsY in Mycobacterium tuberculosis
Authors: Liu, D.F.
History
DepositionApr 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exopolysaccharide phosphotransferase CpsY
B: Exopolysaccharide phosphotransferase CpsY


Theoretical massNumber of molelcules
Total (without water)73,6012
Polymers73,6012
Non-polymers00
Water2,450136
1
A: Exopolysaccharide phosphotransferase CpsY


Theoretical massNumber of molelcules
Total (without water)36,8011
Polymers36,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exopolysaccharide phosphotransferase CpsY


Theoretical massNumber of molelcules
Total (without water)36,8011
Polymers36,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.880, 41.730, 100.440
Angle α, β, γ (deg.)90.00, 93.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exopolysaccharide phosphotransferase CpsY / Stealth protein CpsY


Mass: 36800.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Primary accession P9WGD1
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Tissue: Taxonomic identifier 83332 / Gene: cpsY, Rv0806c
Organ: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Production host: Escherichia coli (E. coli)
References: UniProt: P9WGD1, Transferases; Transferring phosphorus-containing groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Citric acid, 0.05 M BIS-TRIS propane, pH 5.8, 15% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.64→26.1 Å / Num. obs: 81599 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.8
Reflection shellResolution: 1.64→1.67 Å / Rmerge(I) obs: 1.133 / Num. unique obs: 5998

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→26.1 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 4074 4.99 %
Rwork0.2028 --
obs0.204 81575 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→26.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 0 136 4255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074247
X-RAY DIFFRACTIONf_angle_d0.8515764
X-RAY DIFFRACTIONf_dihedral_angle_d5.537555
X-RAY DIFFRACTIONf_chiral_restr0.056607
X-RAY DIFFRACTIONf_plane_restr0.008746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.31661390.29772647X-RAY DIFFRACTION100
1.66-1.680.31171390.29222681X-RAY DIFFRACTION100
1.68-1.70.30761320.27782652X-RAY DIFFRACTION100
1.7-1.720.26711250.26372649X-RAY DIFFRACTION100
1.72-1.750.2621460.26482666X-RAY DIFFRACTION100
1.75-1.770.2941250.2432635X-RAY DIFFRACTION100
1.77-1.80.26741240.22432679X-RAY DIFFRACTION100
1.8-1.830.25431290.22292679X-RAY DIFFRACTION100
1.83-1.860.23261280.21772635X-RAY DIFFRACTION100
1.86-1.890.22841340.2122675X-RAY DIFFRACTION100
1.89-1.920.2691440.21382650X-RAY DIFFRACTION100
1.92-1.960.24011390.21452668X-RAY DIFFRACTION100
1.96-20.25071550.21772651X-RAY DIFFRACTION100
2-2.040.25891580.20362617X-RAY DIFFRACTION100
2.04-2.090.21511360.20032699X-RAY DIFFRACTION100
2.09-2.140.21411430.20472644X-RAY DIFFRACTION100
2.14-2.20.23581270.19762688X-RAY DIFFRACTION100
2.2-2.270.25441310.20162660X-RAY DIFFRACTION100
2.27-2.340.22641550.20092639X-RAY DIFFRACTION100
2.34-2.420.19781430.20392665X-RAY DIFFRACTION100
2.42-2.520.23231340.20692690X-RAY DIFFRACTION100
2.52-2.630.21211310.21912674X-RAY DIFFRACTION100
2.63-2.770.22141280.20852714X-RAY DIFFRACTION100
2.77-2.950.25421480.20642661X-RAY DIFFRACTION100
2.95-3.170.22231670.20472663X-RAY DIFFRACTION100
3.17-3.490.21411580.19462701X-RAY DIFFRACTION100
3.49-3.990.2051360.18722705X-RAY DIFFRACTION100
3.99-5.030.20231460.16562736X-RAY DIFFRACTION100
5.03-26.10.20351740.1882778X-RAY DIFFRACTION99

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