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- PDB-5wb4: Crystal structure of the TarA wall teichoic acid glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 5wb4
TitleCrystal structure of the TarA wall teichoic acid glycosyltransferase
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 / nucleotide binding / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
Function and homology information
Biological speciesThermoanaerobacter italicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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
DepositionJun 27, 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
G: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
H: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,77217
Polymers175,9088
Non-polymers8659
Water7,332407
1
A: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
E: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1694
Polymers43,9772
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-64 kcal/mol
Surface area15530 Å2
MethodPISA
2
B: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
D: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2655
Polymers43,9772
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-81 kcal/mol
Surface area15300 Å2
MethodPISA
3
C: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
F: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1694
Polymers43,9772
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-66 kcal/mol
Surface area15430 Å2
MethodPISA
4
G: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules

H: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1694
Polymers43,9772
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area2710 Å2
ΔGint-65 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.030, 107.790, 89.440
Angle α, β, γ (deg.)90.000, 98.290, 90.000
Int Tables number4
Space group name H-MP1211
Detailsdimer 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: 21988.449 Da / Num. of mol.: 8 / Fragment: TarA / Mutation: C111A
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: D3T4E0, N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% PEG-1000, 100mM phosphate citrate, 200mM lithium sulfate

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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: Apr 4, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→88.51 Å / Num. obs: 189973 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.77 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.153 / Rrim(I) all: 0.172 / Χ2: 1.268 / Net I/σ(I): 7.23 / Num. measured all: 906103 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.054.5310.6182.49132840.8430.69792.8
2.05-2.14.7650.5143.13137620.880.57898.7
2.1-2.174.5520.4293.59132420.9040.48598.1
2.17-2.234.6580.3664.16128960.9320.41297.6
2.23-2.35.0390.3185.01125870.9530.35598.7
2.3-2.395.0110.2785.57122650.9620.31199.1
2.39-2.484.9570.256.09118870.9640.2898.9
2.48-2.584.90.2196.59112900.9710.24598.8
2.58-2.694.7790.1937.21109070.9730.21798.9
2.69-2.824.440.1727.62102160.9750.19597.3
2.82-2.984.9090.1618.6499540.9810.1899.3
2.98-3.164.9940.149.893780.9850.15799.3
3.16-3.374.8920.12310.887970.9860.13899.1
3.37-3.644.7540.11311.7581970.9870.12799.2
3.64-3.994.4630.10512.0874940.9840.11998.3
3.99-4.464.4750.10212.4766920.9860.11596.9
4.46-5.154.8570.10113.1960290.990.11499.3
5.15-6.314.8470.10512.2951050.9890.11799.2
6.31-8.934.4770.09911.9538290.9870.11296.9
8.93-88.515.1360.08714.2921620.9940.09699.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XSCALEdata reduction
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→88.51 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.209 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.246 9663 10 %RANDOM
Rwork0.219 ---
obs0.221 96634 99.1 %-
Displacement parametersBiso max: 95.96 Å2 / Biso mean: 24.96 Å2 / Biso min: 8.66 Å2
Baniso -1Baniso -2Baniso -3
1--9.5349 Å20 Å20.7243 Å2
2--3.5379 Å20 Å2
3---5.997 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2→88.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11591 0 45 407 12043
Biso mean--29.35 25.87 -
Num. residues----1547
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4011SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes307HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1710HARMONIC5
X-RAY DIFFRACTIONt_it11823HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1604SEMIHARMONIC5
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_contact14262SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11823HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg16040HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion17.23
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2496 708 10 %
Rwork0.218 6373 -
all0.2212 7081 -
obs--98.87 %
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)
11.47130.0591-0.70470.5453-0.19761.03880.0419-0.02960.1666-0.0007-0.0185-0.082-0.04440.0705-0.0234-0.11970.00120.0177-0.05190.00120.021236.346913.4011-0.0399
20.6633-0.15130.14020.74720.03341.08550.00780.0009-0.04440.02210.0039-0.0663-0.01490.0505-0.0117-0.0819-0.01260.0462-0.0594-0.00870.0024-8.2018-0.382943.3897
31.1495-0.25010.32261.6789-0.40410.9671-0.06360.14940.1546-0.0834-0.0423-0.09180.0208-0.00930.1059-0.1172-0.01090.0182-0.0860.0132-0.001327.790537.337631.4492
40.70350.11610.25141.9025-0.70831.4556-0.05950.08790.0274-0.2958-0.0444-0.10150.08710.02250.1039-0.099200.0671-0.0877-0.0031-0.0223-10.705724.18831.6441
51.55920.2073-0.33591.3989-0.16740.948-0.056-0.0848-0.34920.1183-0.0336-0.1568-0.0285-0.00240.0896-0.15620.01250.0347-0.10260.00120.052131.2223-10.649712.0244
60.4764-0.00760.21570.7005-0.20151.14270.00990.0182-0.07530.0594-0.0086-0.0605-0.02140.0619-0.0014-0.0938-0.00390.0297-0.0439-0.00450.009730.202312.982443.6747
70.73670.0642-0.17270.5305-0.05560.66420.02170.0210.0624-0.01860.0053-0.0652-0.06140.0087-0.027-0.08210.00030.0338-0.04270.00090.0109-2.25270.2117-0.3054
80.63350.0563-0.02781.38130.1610.816-0.04290.0234-0.0337-0.15850.0245-0.0168-0.00170.02750.0183-0.09330.00080.0391-0.06090.0122-0.00916.870229.969-11.9973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 196
2X-RAY DIFFRACTION2{ B|* }B2 - 195
3X-RAY DIFFRACTION3{ C|* }C3 - 195
4X-RAY DIFFRACTION4{ D|* }D3 - 195
5X-RAY DIFFRACTION5{ E|* }E3 - 195
6X-RAY DIFFRACTION6{ F|* }F2 - 196
7X-RAY DIFFRACTION7{ G|* }G3 - 196
8X-RAY DIFFRACTION8{ H|* }H3 - 195

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