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- PDB-5wfg: Crystal structure of the TarA wall teichoic acid glycosyltransfer... -

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Basic information

Entry
Database: PDB / ID: 5wfg
TitleCrystal structure of the TarA wall teichoic acid glycosyltransferase bound to UDP
ComponentsN-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
KeywordsTRANSFERASE / glycosyltransferase / wall teichoic acid enzyme / Beta-N-acetylmannosaminyltransferase
Function / homologyN-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase activity / Glycosyl transferase WecG/TagA/CpsF / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / Glycosyl transferase WecG/TagA/CpsF family / teichoic acid biosynthetic process / cell wall organization / URIDINE-5'-DIPHOSPHATE / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
Function and homology information
Biological speciesThermoanaerobacter italicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsKattke, M.D. / Cascio, D. / Sawaya, M.R. / Clubb, R.T.
CitationJournal: Plos Pathog. / Year: 2019
Title: Structure and mechanism of TagA, a novel membrane-associated glycosyltransferase that produces wall teichoic acids in pathogenic bacteria.
Authors: Kattke, M.D. / Gosschalk, J.E. / Martinez, O.E. / Kumar, G. / Gale, R.T. / Cascio, D. / Sawaya, M.R. / Philips, M. / Brown, E.D. / Clubb, R.T.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
B: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
C: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
D: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
E: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
F: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,54812
Polymers132,1236
Non-polymers2,4256
Water43224
1
A: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
B: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
C: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2746
Polymers66,0623
Non-polymers1,2123
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-34 kcal/mol
Surface area22020 Å2
MethodPISA
2
D: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
E: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
F: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2746
Polymers66,0623
Non-polymers1,2123
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-36 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.930, 104.210, 90.130
Angle α, β, γ (deg.)90.000, 108.270, 90.000
Int Tables number4
Space group name H-MP1211
Detailstrimer by gel filtration

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Components

#1: Protein
N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / / N-acetylmannosaminyltransferase / UDP-N-acetylmannosamine transferase / UDP-N-acetylmannosamine:N- ...N-acetylmannosaminyltransferase / UDP-N-acetylmannosamine transferase / UDP-N-acetylmannosamine:N-acetylglucosaminyl pyrophosphorylundecaprenol N-acetylmannosaminyltransferase


Mass: 22020.516 Da / Num. of mol.: 6 / Fragment: TarA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter italicus (bacteria) / Strain: DSM 9252 / Ab9 / Gene: Thit_1850 / Plasmid: pMAPLe4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D3T4E0, N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40% PEG-300, 200mM calcium acetate hydrate, 100mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.89→33.03 Å / Num. obs: 44606 / % possible obs: 88.7 % / Observed criterion σ(I): -3 / Redundancy: 1.601 % / Biso Wilson estimate: 89.37 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.105 / Χ2: 2.012 / Net I/σ(I): 7.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.89-2.971.5670.6461.0429870.5940.91179.1
2.97-3.051.5850.5281.2533310.6520.74492.7
3.05-3.141.5960.4151.7632410.7440.58491.4
3.14-3.231.5710.3242.1830800.830.45790
3.23-3.341.5090.2362.8129740.9130.33288.6
3.34-3.461.6060.1873.5129040.9310.26391.6
3.46-3.591.630.1634.1528630.9590.2391.6
3.59-3.731.6210.1195.6726730.9760.16890.5
3.73-3.91.6030.0937.0525500.980.13189.5
3.9-4.091.5440.0748.4424090.9880.10486.9
4.09-4.311.5990.0599.9222640.9920.08488.7
4.31-4.571.6670.05611.4422040.9930.07989.3
4.57-4.891.640.04712.5320340.9950.06689
4.89-5.281.610.04712.419160.9940.06688.1
5.28-5.781.5890.0511.0317040.9950.07186.5
5.78-6.461.6890.04812.9716040.9930.06888.7
6.46-7.461.6390.03915.2213640.9960.05587.5
7.46-9.141.6080.02721.3311370.9970.03985
9.14-12.931.6850.02127.698900.9990.02985.9
12.93-33.031.6160.0226.64770.9980.02886.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.84 Å85.57 Å
Translation2.84 Å85.57 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.6.1phasing
BUSTERrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→33.03 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.41
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2413 10 %RANDOM
Rwork0.2 ---
obs0.204 24132 95.1 %-
Displacement parametersBiso max: 171.19 Å2 / Biso mean: 81.01 Å2 / Biso min: 20.77 Å2
Baniso -1Baniso -2Baniso -3
1--4.9658 Å20 Å2-0.0088 Å2
2---0.6486 Å20 Å2
3---5.6144 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.9→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8216 0 216 24 8456
Biso mean--102.94 43.35 -
Num. residues----1154
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2744SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes190HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1327HARMONIC5
X-RAY DIFFRACTIONt_it8568HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1212SEMIHARMONIC5
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_contact10008SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8568HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11775HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion21.04
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2879 295 9.99 %
Rwork0.2228 2658 -
all0.2295 2953 -
obs--95.88 %
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)
12.5612-1.1654-0.34554.17330.38363.8936-0.1954-0.06960.15340.68260.153-0.252-0.1664-0.01150.04250.52670.0102-0.0351-0.3785-0.0232-0.349482.6654-6.34498.0711
22.76411.4316-0.21083.2447-0.4333.2563-0.1188-0.20370.3178-0.1298-0.04380.5361-0.0655-0.29120.16250.48220.0555-0.0421-0.3655-0.0342-0.296757.2774-20.90580.0467
33.65950.37890.00263.0260.19845.1981-0.1985-0.4814-0.77430.09040.1453-0.17920.35740.17540.05320.45050.12680.0726-0.3940.141-0.270581.4761-36.56448.1573
41.41860.270.84984.27090.96493.21290.01640.0613-0.3029-0.1918-0.0422-0.58160.27310.06580.02590.45340.03050.0424-0.36230.0469-0.311397.2093-34.2501-29.1077
52.66260.361-0.20833.1499-1.01553.6470.05450.1898-0.359-0.2877-0.05250.4839-0.0301-0.486-0.0020.4621-0.0302-0.0114-0.3549-0.0504-0.340969.9339-25.4363-38.3443
64.1112-0.37670.39153.0298-0.31372.1034-0.1250.19540.448-0.17090.08610.0085-0.46690.07830.03890.5136-0.0633-0.0309-0.365-0.0034-0.350990.7003-4.7962-30.9212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 195
2X-RAY DIFFRACTION2{ B|* }B2 - 195
3X-RAY DIFFRACTION3{ C|* }C3 - 195
4X-RAY DIFFRACTION4{ D|* }D3 - 195
5X-RAY DIFFRACTION5{ E|* }E2 - 195
6X-RAY DIFFRACTION6{ F|* }F3 - 195

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