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- PDB-7n41: Crystal structure of TagA with UDP-ManNAc -

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Basic information

Entry
Database: PDB / ID: 7n41
TitleCrystal structure of TagA with UDP-ManNAc
ComponentsN-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / WALL TEICHOIC ACID ENZYME / BETA-N-2 ACETYLMANNOSAMINYLTRANSFERASE / UDP-N-ACETYLMANNOSAMINE
Function / homology
Function and homology information


N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase activity / teichoic acid biosynthetic process / cell wall organization / nucleotide binding
Similarity search - Function
Glycosyl transferase WecG/TagA/CpsF / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase / Glycosyl transferase WecG/TagA/CpsF family
Similarity search - Domain/homology
Chem-UD9 / N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
Similarity search - Component
Biological speciesThermoanaerobacter italicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsMartinez, O.E. / Cascio, D. / Clubb, R.T.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI52217
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Insight into the molecular basis of substrate recognition by the wall teichoic acid glycosyltransferase TagA.
Authors: Martinez, O.E. / Mahoney, B.J. / Goring, A.K. / Yi, S.W. / Tran, D.P. / Cascio, D. / Phillips, M.L. / Muthana, M.M. / Chen, X. / Jung, M.E. / Loo, J.A. / Clubb, R.T.
History
DepositionJun 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5426
Polymers83,7203
Non-polymers1,8223
Water00
1
A: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5142
Polymers27,9071
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5142
Polymers27,9071
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5142
Polymers27,9071
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.640, 113.640, 118.550
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
11(chain A and (resid 2 through 28 or (resid 29...
21(chain B and (resid 2 through 28 or (resid 29...
31(chain C and ((resid 2 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLNGLN(chain A and (resid 2 through 28 or (resid 29...AA2 - 282 - 28
12GLUGLUGLUGLU(chain A and (resid 2 through 28 or (resid 29...AA2929
13GLUGLUVALVAL(chain A and (resid 2 through 28 or (resid 29...AA2 - 1972 - 197
14GLUGLUVALVAL(chain A and (resid 2 through 28 or (resid 29...AA2 - 1972 - 197
15GLUGLUVALVAL(chain A and (resid 2 through 28 or (resid 29...AA2 - 1972 - 197
21GLUGLUGLNGLN(chain B and (resid 2 through 28 or (resid 29...BB2 - 282 - 28
22GLUGLUGLUGLU(chain B and (resid 2 through 28 or (resid 29...BB2929
23GLUGLUARGARG(chain B and (resid 2 through 28 or (resid 29...BB2 - 1992 - 199
31GLUGLUGLUGLU(chain C and ((resid 2 and (name N or name...CC22
32METMETGLYGLY(chain C and ((resid 2 and (name N or name...CC1 - 1951 - 195
33METMETGLYGLY(chain C and ((resid 2 and (name N or name...CC1 - 1951 - 195
34METMETGLYGLY(chain C and ((resid 2 and (name N or name...CC1 - 1951 - 195
35METMETGLYGLY(chain C and ((resid 2 and (name N or name...CC1 - 1951 - 195

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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: 27906.801 Da / Num. of mol.: 3 / Fragment: TagA / Mutation: C111A, I203E, L209Q, L212K, I216E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter italicus (strain DSM 9252 / Ab9) (bacteria)
Strain: DSM 9252 / Ab9 / Gene: Thit_1850 / Plasmid: pMAPLe4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D3T4E0, N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase
#2: Chemical ChemComp-UD9 / (2R,3S,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) / UDP-N-acetyl-alpha-D-mannosamine


Mass: 607.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG-8000, 20% ethylene glycol, 0.05M Tris, 0.04 Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.3→98.42 Å / Num. obs: 13697 / % possible obs: 99.9 % / Redundancy: 7.366 % / Biso Wilson estimate: 84.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.08 / Χ2: 0.911 / Net I/σ(I): 14.74 / Num. measured all: 100887 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.397.2271.1961.477227100210000.6481.28899.8
3.39-3.487.370.8582.1971129669650.7680.92399.9
3.48-3.586.7380.612.9864019529500.8470.66299.8
3.58-3.696.5120.493.5759069089070.9030.53499.9
3.69-3.817.6130.3415.6469059079070.9580.365100
3.81-3.947.9980.2597.769028638630.9760.277100
3.94-4.098.0080.1919.9766078258250.9870.204100
4.09-4.267.9690.13713.3763758008000.9930.147100
4.26-4.457.8520.1215.9560857767750.9940.12899.9
4.45-4.677.6420.09719.3156637417410.9950.104100
4.67-4.927.4820.08821.1553127107100.9950.095100
4.92-5.227.5860.08721.851436786780.9960.093100
5.22-5.587.4930.08421.546986276270.9950.09100
5.58-6.037.3320.07522.7743705975960.9970.08199.8
6.03-6.66.8480.06324.9337805525520.9960.068100
6.6-7.386.0430.05227.9529194904830.9970.05798.6
7.38-8.527.4360.04536.0933464504500.9980.048100
8.52-10.447.4620.0439.8728433813810.9990.042100
10.44-14.766.9570.03739.9221223053050.9990.04100
14.76-98.426.4340.03339.1111711841820.9980.03798.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.82 Å98.42 Å
Translation5.82 Å98.42 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MPK

7mpk


Resolution: 3.3→98.42 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 681 4.97 %
Rwork0.1946 13013 -
obs0.1976 13694 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.3 Å2 / Biso mean: 87.8769 Å2 / Biso min: 26.29 Å2
Refinement stepCycle: final / Resolution: 3.3→98.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 156 0 4612
Biso mean--101.72 --
Num. residues----589
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1749X-RAY DIFFRACTION3.838TORSIONAL
12B1749X-RAY DIFFRACTION3.838TORSIONAL
13C1749X-RAY DIFFRACTION3.838TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.560.31781470.25525522699
3.56-3.910.26991410.212625522693
3.91-4.480.27591180.178225852703
4.48-5.640.2651230.186526282751
5.64-98.420.21471520.183926962848
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)
10.03240.0141-0.00030.02410.02640.02160.2788-0.2613-0.37750.18480.136-0.125-0.08570.23110.00081.1018-0.19930.11190.47550.01310.855410.4758-72.8188-8.3731
20.5734-0.1741-0.15890.05260.04970.0460.43670.0411-0.4289-0.0349-0.0831-0.40090.4228-0.071-0.04441.695-0.56170.20240.836-0.22620.966-1.0374-80.8107-4.7286
30.514-0.1635-0.00530.1155-0.09980.29020.1390.0381-0.33390.5053-0.40240.27440.3004-0.1147-0.01631.2617-0.30360.08550.5149-0.05280.68047.5773-67.3318-5.8784
40.10270.05720.12660.04320.05610.21620.0732-0.30270.3404-0.0205-0.16180.4875-0.1609-0.56540.0081.691-0.89950.32391.5038-0.55351.6992-12.6784-75.5237-2.8306
50.00190.00330.00710.00710.0190.05420.0937-0.0157-0.03020.13580.0099-0.0113-0.08040.0427-0.00061.4274-0.62830.04362.4598-0.43331.5074-21.0186-71.1031-0.72
60.7032-0.7372-0.02751.02730.18720.1123-0.3176-0.2314-0.15510.6287-0.16130.03270.4889-0.1241-0.11531.9258-1.0560.5551.7522-0.44351.2194-11.9669-75.713310.7921
70.0392-0.02880.00760.06620.01660.0145-0.3559-0.0756-0.43310.1569-0.0324-0.09120.3460.1624-0.0021.511-0.45610.40090.99480.02480.6414-0.9051-74.74969.2508
80.0176-0.01780.00230.0165-0.00490.0136-0.1494-0.0702-0.0139-0.1757-0.3101-0.0568-0.0948-0.52240.00171.6571-0.4472-0.0351.1259-0.36391.0536-10.4508-68.6967-0.5384
90.00310.0079-0.00570.02170.00710.0422-0.1949-0.0046-0.3195-0.04780.01720.1340.1382-0.46670.00030.8961-0.1945-0.06310.62560.00350.61287.3458-48.4693-2.7318
100.59860.27780.71460.70760.71181.1236-0.27060.0445-0.0753-1.0278-0.04720.3168-0.1496-0.62390.04130.9377-0.0254-0.10390.45130.03150.50236.5177-33.82350.2602
111.8386-0.4003-0.48310.1340.05560.2505-0.105-0.37130.2809-0.41090.6313-0.37740.3853-0.00980.11190.9487-0.05980.05530.42280.05430.702317.205-46.98250.958
120.0506-0.0090.01620.01480.00860.0574-0.07150.05940.4644-0.39730.046-0.3173-0.4638-0.56640.00011.4339-0.11820.05130.5432-0.02920.60037.5791-49.1937-11.9195
130.06870.02960.01380.51240.23380.141-0.15670.30230.1017-0.75720.04570.1259-0.2786-0.0310.07281.3726-0.36090.359-0.38550.16850.509715.4556-25.6856-5.0595
140.00990.0821-0.02620.7509-0.26410.0919-0.10570.08530.02530.0490.0639-0.1893-0.30190.09420.0742.0152-0.48480.54950.8466-0.08720.872222.1845-20.2601-9.2131
150.33570.1971-0.44910.1324-0.24850.60080.04150.0538-0.358-0.81420.138-0.6923-0.25150.33680.27061.0911-0.10520.22470.2153-0.05460.865722.8179-23.07-0.798
160.0590.07760.01430.1437-0.03950.12350.0175-0.26830.10670.31570.0069-0.5286-0.0972-0.0675-0.00070.7245-0.0994-0.00790.3843-0.03440.639422.5566-26.76387.2646
170.0075-0.0136-0.00250.03490.01450.00730.1847-0.2124-0.47560.0067-0.0436-0.30360.1535-0.0862-00.4891-0.1836-0.02790.4943-0.13020.801221.2351-37.41017.5567
181.30030.25940.06080.532-0.18791.56930.2387-0.10130.0312-0.34650.3184-0.77790.1365-0.10780.19350.7373-0.09720.13350.26830.03820.480219.516-30.2631-0.9036
190.09520.0015-0.06840.09410.06740.80940.3635-0.02970.37150.19090.053-0.7078-1.140.52650.30911.2024-0.37650.30860.6032-0.01720.970831.8399-62.4347-15.1666
200.8163-0.24830.65350.82910.44611.13980.23670.40780.36060.37970.1742-1.01250.10430.89521.40050.5408-0.31990.04570.6034-0.11130.740340.7572-78.9242-16.5438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 15 )C1 - 15
2X-RAY DIFFRACTION2chain 'C' and (resid 16 through 39 )C16 - 39
3X-RAY DIFFRACTION3chain 'C' and (resid 40 through 85 )C40 - 85
4X-RAY DIFFRACTION4chain 'C' and (resid 86 through 112 )C86 - 112
5X-RAY DIFFRACTION5chain 'C' and (resid 113 through 124 )C113 - 124
6X-RAY DIFFRACTION6chain 'C' and (resid 125 through 161 )C125 - 161
7X-RAY DIFFRACTION7chain 'C' and (resid 162 through 181 )C162 - 181
8X-RAY DIFFRACTION8chain 'C' and (resid 182 through 195 )C182 - 195
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 15 )A2 - 15
10X-RAY DIFFRACTION10chain 'A' and (resid 16 through 39 )A16 - 39
11X-RAY DIFFRACTION11chain 'A' and (resid 40 through 66 )A40 - 66
12X-RAY DIFFRACTION12chain 'A' and (resid 67 through 85 )A67 - 85
13X-RAY DIFFRACTION13chain 'A' and (resid 86 through 112 )A86 - 112
14X-RAY DIFFRACTION14chain 'A' and (resid 113 through 124 )A113 - 124
15X-RAY DIFFRACTION15chain 'A' and (resid 125 through 139 )A125 - 139
16X-RAY DIFFRACTION16chain 'A' and (resid 140 through 165 )A140 - 165
17X-RAY DIFFRACTION17chain 'A' and (resid 166 through 175 )A166 - 175
18X-RAY DIFFRACTION18chain 'A' and (resid 176 through 197 )A176 - 197
19X-RAY DIFFRACTION19chain 'B' and (resid 2 through 97 )B2 - 97
20X-RAY DIFFRACTION20chain 'B' and (resid 98 through 199 )B98 - 199

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