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- PDB-7xtn: Crystal structure of the C-terminal domain of Bombyx mori N-acety... -

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Basic information

Entry
Database: PDB / ID: 7xtn
TitleCrystal structure of the C-terminal domain of Bombyx mori N-acetylglucosaminyltransferase IV in complex with N-acetylglucosamine
ComponentsN-acetylglucosaminyltransferase IV
KeywordsSUGAR BINDING PROTEIN / glycosyltransferase / N-glycan / N-glycosylation / Golgi / N-acetylglucosamine / carbohydrate-binding module / lectin
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMiyazaki, T. / Oka, N. / Mori, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Glycobiology / Year: 2022
Title: Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family.
Authors: Oka, N. / Mori, S. / Ikegaya, M. / Park, E.Y. / Miyazaki, T.
History
DepositionMay 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosaminyltransferase IV
B: N-acetylglucosaminyltransferase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7718
Polymers38,0802
Non-polymers6916
Water3,855214
1
A: N-acetylglucosaminyltransferase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4485
Polymers19,0401
Non-polymers4074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetylglucosaminyltransferase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3233
Polymers19,0401
Non-polymers2832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.697, 64.098, 79.148
Angle α, β, γ (deg.)90.000, 95.891, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-acetylglucosaminyltransferase IV


Mass: 19040.176 Da / Num. of mol.: 2 / Fragment: CBM domain
Source method: isolated from a genetically manipulated source
Details: GB:BDI24347.2 / Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: MGAT4 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MES-NaOH, pH 7.0, 12%(w/v) PEG20000, 10 mM N-acetylglucosamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→39.37 Å / Num. obs: 113597 / % possible obs: 98.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 18.1
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 15961 / CC1/2: 0.782 / Rpim(I) all: 0.336 / Rrim(I) all: 0.879 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 1.15→32.545 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.451 / SU ML: 0.032 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2087 5719 5.035 %
Rwork0.1933 107860 -
all0.194 --
obs-113579 98.625 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 18.769 Å2
Baniso -1Baniso -2Baniso -3
1-0.534 Å20 Å2-0.401 Å2
2--0.215 Å2-0 Å2
3----0.653 Å2
Refinement stepCycle: LAST / Resolution: 1.15→32.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 46 214 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132653
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152377
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.6653606
X-RAY DIFFRACTIONr_angle_other_deg1.4231.5945483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7335307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02223.101158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61215413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8221512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined0.20.2394
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22195
X-RAY DIFFRACTIONr_nbtor_refined0.180.21229
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2162
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.239
X-RAY DIFFRACTIONr_nbd_other0.2090.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.210
X-RAY DIFFRACTIONr_mcbond_it0.8111.0971211
X-RAY DIFFRACTIONr_mcbond_other0.811.0961210
X-RAY DIFFRACTIONr_mcangle_it1.3171.6451511
X-RAY DIFFRACTIONr_mcangle_other1.3171.6461512
X-RAY DIFFRACTIONr_scbond_it1.2641.3241442
X-RAY DIFFRACTIONr_scbond_other1.2631.3261443
X-RAY DIFFRACTIONr_scangle_it1.9981.9122090
X-RAY DIFFRACTIONr_scangle_other1.9981.9132091
X-RAY DIFFRACTIONr_lrange_it4.19913.6772854
X-RAY DIFFRACTIONr_lrange_other4.09613.252813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.2884200.2857566X-RAY DIFFRACTION93.7214
1.18-1.2120.2894110.2737560X-RAY DIFFRACTION96.2449
1.212-1.2470.273770.2657478X-RAY DIFFRACTION97.9426
1.247-1.2860.2513680.2517294X-RAY DIFFRACTION98.0924
1.286-1.3280.2673500.2397101X-RAY DIFFRACTION98.5973
1.328-1.3740.2433630.2236921X-RAY DIFFRACTION98.7259
1.374-1.4260.253070.2126683X-RAY DIFFRACTION98.8685
1.426-1.4850.2283370.1996430X-RAY DIFFRACTION99.3978
1.485-1.5510.2233370.1926162X-RAY DIFFRACTION99.4339
1.551-1.6260.1993030.1895909X-RAY DIFFRACTION99.5513
1.626-1.7140.1872970.185665X-RAY DIFFRACTION99.8158
1.714-1.8180.2043130.1885295X-RAY DIFFRACTION99.8042
1.818-1.9430.1932690.1875022X-RAY DIFFRACTION99.9811
1.943-2.0990.2082660.1794628X-RAY DIFFRACTION100
2.099-2.2990.1962520.1744310X-RAY DIFFRACTION100
2.299-2.570.2092040.1863908X-RAY DIFFRACTION100
2.57-2.9670.2181830.1963463X-RAY DIFFRACTION99.8904
2.967-3.6330.1951680.1872925X-RAY DIFFRACTION99.8064
3.633-5.1330.1651140.1712264X-RAY DIFFRACTION100
5.133-32.5450.245800.2111277X-RAY DIFFRACTION99.7061
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)
10.1270.2087-0.24450.9060.04761.03870.0426-0.00930.00190.1952-0.03710.16060.0165-0.0525-0.00560.04490.00330.03150.06290.0150.123210.33341.656715.3494
20.2835-0.04430.18071.01410.25471.15950.00560.0027-0.0307-0.06050.00850.0058-0.0210.0571-0.01410.0355-0.0014-0.0010.0511-0.00750.06617.5730.33072.7247
30.040.1456-0.10121.22960.11431.8081-0.00030.04640.0432-0.0935-0.02420.20020.0718-0.2120.02450.01960.0176-0.00170.14140.02090.074718.4873-32.85927.5929
40.2044-0.03270.01841.38210.13611.20910.04440.06990.04930.1653-0.0815-0.03890.05170.12890.03710.0376-0.001-0.00130.07930.010.06729.4354-29.754735.9223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA392 - 460
2X-RAY DIFFRACTION2ALLA461 - 547
3X-RAY DIFFRACTION3ALLB401 - 448
4X-RAY DIFFRACTION4ALLB449 - 548

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