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- PDB-6e4q: Crystal Structure of the Drosophila Melanogaster Polypeptide N-Ac... -

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Basic information

Entry
Database: PDB / ID: 6e4q
TitleCrystal Structure of the Drosophila Melanogaster Polypeptide N-Acetylgalactosaminyl Transferase PGANT9A in Complex with UDP and Mn2+
Componentspolypeptide N-acetylgalactosaminyltransferase 9
KeywordsTRANSFERASE / O-Glycosyltransferase / GT-A fold catalytic domain / Ricin B-type lectin domain / metal-dependent enzyme
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Golgi cisterna / sexual reproduction / protein O-linked glycosylation / carbohydrate binding / Golgi membrane / Golgi apparatus / membrane / metal ion binding / cytosol
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Putative polypeptide N-acetylgalactosaminyltransferase 9
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.799 Å
AuthorsSamara, N.L. / Tabak, L.A. / Ten Hagen, K.G.
CitationJournal: Nat Commun / Year: 2018
Title: A molecular switch orchestrates enzyme specificity and secretory granule morphology.
Authors: Ji, S. / Samara, N.L. / Revoredo, L. / Zhang, L. / Tran, D.T. / Muirhead, K. / Tabak, L.A. / Ten Hagen, K.G.
History
DepositionJul 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: polypeptide N-acetylgalactosaminyltransferase 9
B: polypeptide N-acetylgalactosaminyltransferase 9
C: polypeptide N-acetylgalactosaminyltransferase 9
D: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,37724
Polymers233,0994
Non-polymers3,27820
Water3,495194
1
A: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0796
Polymers58,2751
Non-polymers8045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1096
Polymers58,2751
Non-polymers8345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0796
Polymers58,2751
Non-polymers8045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: polypeptide N-acetylgalactosaminyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1096
Polymers58,2751
Non-polymers8345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.286, 168.756, 153.099
Angle α, β, γ (deg.)90.00, 106.28, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
polypeptide N-acetylgalactosaminyltransferase 9 / / pp-GaNTase 9 / Protein-UDP acetylgalactosaminyltransferase 9 / UDP-GalNAc:polypeptide N- ...pp-GaNTase 9 / Protein-UDP acetylgalactosaminyltransferase 9 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 9


Mass: 58274.699 Da / Num. of mol.: 4 / Fragment: Catalytic domain, Ricin B-type lectin Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pgant9, CG30463 / Plasmid: pPICZ alpha A / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: Q8MRC9, polypeptide N-acetylgalactosaminyltransferase
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 210 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.36 Å3/Da / Density % sol: 63.38 % / Mosaicity: 0 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3350, 0.2 M sodium malonate,20 mM strontium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→19.95 Å / Num. obs: 71031 / % possible obs: 93.8 % / Redundancy: 1 % / Biso Wilson estimate: 39.65 Å2 / Net I/σ(I): 4.9 / Num. measured all: 71031
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
2.8-2.8613366169.2
13.42-19.951500170.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.799→19.954 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 3521 4.97 %
Rwork0.1896 --
obs0.1931 71031 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.799→19.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16212 0 196 194 16602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01316905
X-RAY DIFFRACTIONf_angle_d1.1622856
X-RAY DIFFRACTIONf_dihedral_angle_d20.49110011
X-RAY DIFFRACTIONf_chiral_restr0.0632353
X-RAY DIFFRACTIONf_plane_restr0.0072935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7986-2.83030.37831660.28713154X-RAY DIFFRACTION67
2.8303-2.86350.39081730.29143412X-RAY DIFFRACTION71
2.8635-2.89830.37651700.28073584X-RAY DIFFRACTION76
2.8983-2.93490.3841970.27923692X-RAY DIFFRACTION78
2.9349-2.97340.30541820.27943959X-RAY DIFFRACTION83
2.9734-3.0140.42292050.26264015X-RAY DIFFRACTION84
3.014-3.05690.34492360.25434181X-RAY DIFFRACTION88
3.0569-3.10240.30482390.25644200X-RAY DIFFRACTION90
3.1024-3.15070.33282370.25344391X-RAY DIFFRACTION92
3.1507-3.20210.34972300.26164469X-RAY DIFFRACTION95
3.2021-3.25710.33052700.22914624X-RAY DIFFRACTION97
3.2571-3.31610.31292640.21554654X-RAY DIFFRACTION99
3.3161-3.37950.30382070.21984685X-RAY DIFFRACTION100
3.3795-3.44820.30452430.21664736X-RAY DIFFRACTION100
3.4482-3.52280.27112330.21024800X-RAY DIFFRACTION100
3.5228-3.60420.28452180.19354731X-RAY DIFFRACTION100
3.6042-3.69380.25522610.18334686X-RAY DIFFRACTION100
3.6938-3.7930.26762580.1734744X-RAY DIFFRACTION100
3.793-3.90380.25432750.16574676X-RAY DIFFRACTION100
3.9038-4.02890.22452870.15464694X-RAY DIFFRACTION100
4.0289-4.17160.19992410.14914702X-RAY DIFFRACTION100
4.1716-4.3370.232510.15824721X-RAY DIFFRACTION100
4.337-4.53220.21642450.15084742X-RAY DIFFRACTION100
4.5322-4.7680.19842430.14374768X-RAY DIFFRACTION100
4.768-5.06220.21932400.1484720X-RAY DIFFRACTION100
5.0622-5.44570.20132590.15054749X-RAY DIFFRACTION100
5.4457-5.98030.23312670.1744682X-RAY DIFFRACTION100
5.9803-6.81530.23672130.1854735X-RAY DIFFRACTION100
6.8153-8.47560.21612070.16834795X-RAY DIFFRACTION100
8.4756-19.95470.20762550.16814673X-RAY DIFFRACTION99
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)
11.27730.2255-0.70190.95450.14220.63820.00450.0746-0.1194-0.13120.00390.03230.18370.0868-0.02620.50630.0096-0.13710.34340.00470.217611.44312.415453.5279
23.2717-1.788-1.33092.5316-0.662.507-0.0595-0.36570.29650.0349-0.0751-0.1529-0.0710.08520.10710.5169-0.0183-0.09640.2767-0.03830.19790.82644.444462.3913
31.3767-0.48271.20971.7825-0.47042.3276-0.0986-0.2023-0.01690.55150.0204-0.0951-0.176-0.1980.08140.7022-0.0202-0.0280.2802-0.00850.26670.3757-5.124886.9592
42.63840.0488-0.38860.62170.01890.4769-0.00570.1579-0.0495-0.1846-0.0066-0.0443-0.1396-0.07910.01430.81370.0235-0.14310.27340.00940.284621.3445-41.260375.0765
51.03221.2946-0.29021.6877-0.52121.42140.0568-0.2074-0.08140.3646-0.0985-0.2369-0.0073-0.07110.04250.75280.0544-0.18960.3147-0.00130.31576.501-49.923888.7942
62.0506-0.32090.22013.55810.1433.68370.02980.0222-0.0598-0.07620.0214-0.17410.2778-0.0581-0.06070.4622-0.0025-0.13720.3094-0.01780.2361-5.5825-72.908674.4852
72.2081-0.4029-0.70920.826-0.39710.54010.06930.23790.15680.0277-0.0454-0.0458-0.20740.0052-0.05110.5534-0.0395-0.09830.3030.02140.227243.050618.1387109.2285
83.33950.30330.34831.3159-0.42670.8730.16310.1055-0.1283-0.0668-0.0730.04350.2917-0.1065-0.07760.6365-0.0137-0.0940.2783-0.01930.201321.016116.9809114.6818
92.36230.96421.30672.8589-0.00663.85760.05550.08740.03360.0156-0.10310.03970.38240.01960.0390.87420.0718-0.21190.3385-0.030.30965.735332.938294.0399
101.7637-0.2805-0.7750.53990.18391.08070.0033-0.2720.14640.2520.1178-0.35780.04160.2365-0.10550.69510.0056-0.28460.3189-0.0460.525529.5848-106.731989.9172
116.5399-0.73050.66816.0079-1.91882.0661-0.2710.6265-0.1529-0.29010.5422-0.40840.24690.133-0.23920.60490.0476-0.14250.3364-0.07790.291111.3202-101.810291.5685
122.08390.1082-0.35161.66120.58250.9672-0.0339-0.09310.16160.11750.05110.07430.1707-0.0157-0.04030.60170.0046-0.25030.3229-0.00560.32559.7222-95.916997.4668
134.7313-0.14972.25843.702-1.20674.1828-0.26990.13880.2539-0.08270.14260.02340.01610.28670.10690.5857-0.018-0.13420.30440.00860.235417.1564-74.1975112.8921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 143 through 371 )
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 454 )
3X-RAY DIFFRACTION3chain 'A' and (resid 455 through 650 )
4X-RAY DIFFRACTION4chain 'B' and (resid 143 through 398 )
5X-RAY DIFFRACTION5chain 'B' and (resid 399 through 515 )
6X-RAY DIFFRACTION6chain 'B' and (resid 516 through 650 )
7X-RAY DIFFRACTION7chain 'C' and (resid 143 through 363 )
8X-RAY DIFFRACTION8chain 'C' and (resid 364 through 523 )
9X-RAY DIFFRACTION9chain 'C' and (resid 524 through 650 )
10X-RAY DIFFRACTION10chain 'D' and (resid 143 through 398 )
11X-RAY DIFFRACTION11chain 'D' and (resid 399 through 425 )
12X-RAY DIFFRACTION12chain 'D' and (resid 426 through 523 )
13X-RAY DIFFRACTION13chain 'D' and (resid 524 through 650 )

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