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- PDB-8e37: Structure of Campylobacter concisus wild-type SeMet PglC -

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Basic information

Entry
Database: PDB / ID: 8.0E+37
TitleStructure of Campylobacter concisus wild-type SeMet PglC
ComponentsN,N'-diacetylbacilliosaminyl-1-phosphate transferase
KeywordsMEMBRANE PROTEIN / Campylobacter / glycoconjugate / phosphoglycosyltransferase
Function / homologyundecaprenyl phosphate N,N'-diacetylbacillosamine 1-phosphate transferase / N,N'-diacetylbacilliosaminyl-1-phosphate transferase activity / Bacterial sugar transferase / Bacterial sugar transferase / membrane => GO:0016020 / N,N'-diacetylbacilliosaminyl-1-phosphate transferase
Function and homology information
Biological speciesCampylobacter concisus 13826 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsVuksanovic, N. / Ray, L.C. / Imperiali, B. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM131627 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble.
Authors: Majumder, A. / Vuksanovic, N. / Ray, L.C. / Bernstein, H.M. / Allen, K.N. / Imperiali, B. / Straub, J.E.
History
DepositionAug 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
A: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
C: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
D: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
E: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
F: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
G: N,N'-diacetylbacilliosaminyl-1-phosphate transferase
H: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)188,9438
Polymers188,9438
Non-polymers00
Water00
1
B: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: N,N'-diacetylbacilliosaminyl-1-phosphate transferase


Theoretical massNumber of molelcules
Total (without water)23,6181
Polymers23,6181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.820, 142.820, 192.563
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: -1 - 183 / Label seq-ID: 3 - 187

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBA
3chain CCC
4chain DDD
5chain EEE
6chain FFF
7chain GGG
8chain HHH

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Components

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


Mass: 23617.846 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter concisus 13826 (Campylobacter)
Strain: 13826 / Gene: pglC, CCC13826_0450 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A7ZET4, undecaprenyl phosphate N,N'-diacetylbacillosamine 1-phosphate transferase
Has ligand of interestN

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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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.0, 0.3 M MgCl2, 27% PEG 3350,1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→47.7 Å / Num. obs: 38779 / % possible obs: 82.76 % / Redundancy: 1.9 % / Biso Wilson estimate: 83.8 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.105 / Net I/σ(I): 14.2
Reflection shellResolution: 3.01→3.121 Å / Num. unique obs: 3544 / CC1/2: 0.553

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W7L

5w7l
PDB Unreleased entry


Resolution: 3.01→37.99 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2958 3720 5.22 %
Rwork0.2657 67491 -
obs0.2672 38391 82.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.78 Å2 / Biso mean: 111.5296 Å2 / Biso min: 55.94 Å2
Refinement stepCycle: final / Resolution: 3.01→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12088 0 0 0 12088
Num. residues----1480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4320X-RAY DIFFRACTION5.474TORSIONAL
12B4320X-RAY DIFFRACTION5.474TORSIONAL
13C4320X-RAY DIFFRACTION5.474TORSIONAL
14D4320X-RAY DIFFRACTION5.474TORSIONAL
15E4320X-RAY DIFFRACTION5.474TORSIONAL
16F4320X-RAY DIFFRACTION5.474TORSIONAL
17G4320X-RAY DIFFRACTION5.474TORSIONAL
18H4320X-RAY DIFFRACTION5.474TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.01-3.050.37121190.35812077219667
3.05-3.090.34891240.34492189231373
3.09-3.130.33691190.35222242236173
3.13-3.180.36761240.32962341246577
3.18-3.230.4431430.33392373251679
3.23-3.280.30811380.31742485262382
3.28-3.330.32481430.33112478262180
3.33-3.390.35571340.30552429256381
3.39-3.450.35661410.30962580272184
3.45-3.520.30911500.29732606275686
3.52-3.590.32631420.3112577271984
3.59-3.670.34191450.2992595274085
3.67-3.750.34651530.2852664281788
3.75-3.840.30581330.26772628276187
3.84-3.950.31981520.26762647279987
3.95-4.060.32361500.24822666281687
4.06-4.20.2521460.25672619276586
4.2-4.340.32411260.22932482260881
4.35-4.520.28621430.23622570271385
4.52-4.720.25661340.24732618275286
4.72-4.970.26741440.26342510265484
4.97-5.280.2781440.27992632277686
5.28-5.690.30251450.28062600274585
5.69-6.260.29051300.28672494262482
6.26-7.160.36071410.2742519266083
7.16-90.23431400.21832526266683
9.01-37.990.25541170.23212344246177
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.70810.51631.42981.5283-0.36633.4512-0.04340.52310.5458-0.1059-0.06370.2523-0.4507-0.04960.16890.5595-0.04820.01470.54130.03360.7458-8.077-18.0526.337
21.66310.5550.50153.59530.83342.02070.0498-0.14120.08470.2509-0.21490.5292-0.5138-0.08980.19920.7635-0.15070.01440.69510.10270.7551-52.599-1.75137.822
31.48141.09320.19612.8284-1.18672.1590.042-0.61820.48860.7915-0.20841.362-0.6735-0.49890.16890.9279-0.02240.31440.7847-0.19451.0883-43.43310.096-18.01
42.17112.53120.45281.338-1.20772.7731-0.52131.0612-1.3591-0.89580.5479-1.15670.46370.8276-0.07981.0064-0.14370.38241.0398-0.62291.4793-76.70231.54214.711
54.6593-0.1490.34223.3762-0.19523.1796-0.06681.19570.3963-0.41940.13960.6925-0.067-0.9418-0.1040.6162-0.1634-0.05691.22480.22730.7966-42.03843.63923.193
61.6912-0.18940.19920.30831.77354.1825-0.03470.4770.4954-0.303-0.09280.2954-0.063-1.41580.13340.7476-0.1625-0.19891.10740.25820.9298-78.026-19.77424.217
72.38462.5054-1.22743.805-0.74971.01240.3681-0.2811-0.99690.7728-0.4121-0.82650.59010.2330.05590.8927-0.1127-0.2550.67540.13130.9977-25.59916.58144.399
82.8813-0.3041-0.62420.8936-0.15231.57550.03720.3548-1.0912-0.3204-0.0111-0.38670.08780.14920.04150.8061-0.1139-0.09070.8141-0.05141.1233-37.453-33.1622.576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 3:183 )B3 - 183
2X-RAY DIFFRACTION2( CHAIN A AND RESID 3:183 )A3 - 183
3X-RAY DIFFRACTION3( CHAIN C AND RESID 3:183 )C3 - 183
4X-RAY DIFFRACTION4( CHAIN D AND RESID 3:183 )D3 - 183
5X-RAY DIFFRACTION5( CHAIN E AND RESID 3:183 )E3 - 183
6X-RAY DIFFRACTION6( CHAIN F AND RESID 3:183 )F3 - 183
7X-RAY DIFFRACTION7( CHAIN G AND RESID 3:183 )G3 - 183
8X-RAY DIFFRACTION8( CHAIN H AND RESID 3:183 )H3 - 183

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