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- PDB-8g1n: Structure of Campylobacter concisus PglC I57M/Q175M Variant with ... -

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Basic information

Entry
Database: PDB / ID: 8g1n
TitleStructure of Campylobacter concisus PglC I57M/Q175M Variant with modeled C-terminus
ComponentsN,N'-diacetylbacilliosaminyl-1-phosphate transferase
KeywordsMEMBRANE PROTEIN / phosphoglycosyl transferase / reentrant membrane helix
Function / homologyundecaprenyl phosphate N,N'-diacetylbacillosamine 1-phosphate transferase / N,N'-diacetylbacilliosaminyl-1-phosphate transferase activity / Bacterial sugar transferase / Bacterial sugar transferase / membrane / metal ion binding / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / PHOSPHATE ION / N,N'-diacetylbacilliosaminyl-1-phosphate transferase
Function and homology information
Biological speciesCampylobacter concisus 13826 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å
AuthorsDodge, G.J. / Ray, L.C. / Das, D. / Imperiali, B. / Allen, K.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131627 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM039334 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134576 United States
CitationJournal: Protein Sci. / Year: 2023
Title: Co-conserved sequence motifs are predictive of substrate specificity in a family of monotopic phosphoglycosyl transferases.
Authors: Anderson, A.J. / Dodge, G.J. / Allen, K.N. / Imperiali, B.
History
DepositionFeb 2, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionMay 31, 2023ID: 5W7L
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
B: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6248
Polymers46,9032
Non-polymers1,7226
Water36020
1
A: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4575
Polymers23,4511
Non-polymers1,0054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1683
Polymers23,4511
Non-polymers7162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.802, 70.802, 188.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Mass: 23451.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter concisus 13826 (Campylobacter)
Gene: pglC, CCC13826_0450 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A7ZET4, undecaprenyl phosphate N,N'-diacetylbacillosamine 1-phosphate transferase

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Non-polymers , 5 types, 26 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Bis-Tris 0.1 M, magnesium chloride hexahydrate 0.4 M, PEG 3350 23%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.74→62.814 Å / Num. obs: 27735 / % possible obs: 99.95 % / Redundancy: 18.1 % / Biso Wilson estimate: 68.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.032 / Net I/σ(I): 21.4
Reflection shellResolution: 2.74→2.87 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.033 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1941 / CC1/2: 0.714 / Rpim(I) all: 0.434

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.74→62.81 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2969 723 5 %
Rwork0.2585 --
obs0.2604 14453 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→62.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 58 20 3223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023259
X-RAY DIFFRACTIONf_angle_d0.4754372
X-RAY DIFFRACTIONf_dihedral_angle_d13.3611244
X-RAY DIFFRACTIONf_chiral_restr0.037481
X-RAY DIFFRACTIONf_plane_restr0.004545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.950.36341120.29992530X-RAY DIFFRACTION90
2.95-3.250.3281620.28152630X-RAY DIFFRACTION95
3.25-3.720.34971510.2912739X-RAY DIFFRACTION97
3.72-4.680.28211420.23592836X-RAY DIFFRACTION99
4.69-62.810.26761560.25012995X-RAY DIFFRACTION99

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