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- PDB-4m90: crystal structure of oxidized hN33/Tusc3 -

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Basic information

Entry
Database: PDB / ID: 4m90
Titlecrystal structure of oxidized hN33/Tusc3
ComponentsTumor suppressor candidate 3
KeywordsOXIDOREDUCTASE / Thioredoxin-like fold / Redox active / endoplasmic reticulum
Function / homology
Function and homology information


Asparagine N-linked glycosylation / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / transmembrane transport / cognition / Maturation of spike protein ...Asparagine N-linked glycosylation / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / transmembrane transport / cognition / Maturation of spike protein / endoplasmic reticulum membrane / mitochondrion / plasma membrane
Similarity search - Function
Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / Thioredoxin-like superfamily
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TUSC3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R.
CitationJournal: Structure / Year: 2014
Title: Structural basis of substrate specificity of human oligosaccharyl transferase subunit n33/tusc3 and its role in regulating protein N-glycosylation.
Authors: Mohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor suppressor candidate 3


Theoretical massNumber of molelcules
Total (without water)19,1421
Polymers19,1421
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.660, 62.477, 64.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsSububit of the human oligosaccharyl transferase complex

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Components

#1: Protein Tumor suppressor candidate 3 / Magnesium uptake/transporter TUSC3 / Protein N33


Mass: 19141.865 Da / Num. of mol.: 1 / Fragment: unp residues 44-194 / Mutation: C82S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUSC3, N33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13454
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M KSCN, 10.5% PEG 8K, 10% PEG 1K in 100 mM cacodylic acid-NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→64 Å / Num. all: 21247 / Num. obs: 21141 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.063 / Net I/σ(I): 12.5
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.593 / % possible all: 99.6

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Processing

Software
NameClassification
PHASERphasing
PHENIXrefinement
REFMACrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4M8G

4m8g


Resolution: 1.6→32.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.942 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22003 443 2.1 %RANDOM
Rwork0.18484 ---
obs0.18552 20596 98.88 %-
all-20596 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0 Å2
2--0.19 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1263 0 0 136 1399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0210.0191317
X-RAY DIFFRACTIONf_bond_other_d0.0020.021234
X-RAY DIFFRACTIONf_angle_refined_deg1.7811.9251779
X-RAY DIFFRACTIONf_angle_other_deg0.8913.0012822
X-RAY DIFFRACTIONf_dihedral_angle_1_deg6.5085159
X-RAY DIFFRACTIONf_dihedral_angle_2_deg31.85822.91772
X-RAY DIFFRACTIONf_dihedral_angle_3_deg12.83515229
X-RAY DIFFRACTIONf_dihedral_angle_4_deg19.1221514
X-RAY DIFFRACTIONf_chiral_restr0.1180.2180
X-RAY DIFFRACTIONf_gen_planes_refined0.0090.0211523
X-RAY DIFFRACTIONf_gen_planes_other0.0010.02355
X-RAY DIFFRACTIONf_nbd_refined
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it3.0941.36621
X-RAY DIFFRACTIONf_mcbond_other3.0611.358620
X-RAY DIFFRACTIONf_mcangle_it5.2552.022776
X-RAY DIFFRACTIONf_mcangle_other5.2582.027777
X-RAY DIFFRACTIONf_scbond_it3.5781.813696
X-RAY DIFFRACTIONf_scbond_other3.5751.814696
X-RAY DIFFRACTIONf_scangle_it
X-RAY DIFFRACTIONf_scangle_other5.8682.5391000
X-RAY DIFFRACTIONf_long_range_B_refined10.62613.4911620
X-RAY DIFFRACTIONf_long_range_B_other10.6312.631556
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 36 -
Rwork0.285 1479 -
obs--99.54 %
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)
13.26063.2275-1.45255.32220.97583.5590.19780.228-0.14250.91690.2877-0.47110.5698-0.1535-0.48550.46970.10160.06950.13760.08170.2443-9.493-4.415630.2751
20.2573-0.3150.00170.8045-0.25040.2261-0.0907-0.09810.02010.25460.0887-0.0189-0.01760.04350.00190.1480.01780.00130.1255-0.01650.08991.93938.012624.8271
31.31031.6084-4.82221.9847-5.909517.7580.0166-0.0737-0.0364-0.0003-0.1408-0.0436-0.09010.22220.12420.06720.10590.02230.24820.00980.0652-13.128612.950132.5843
40.1725-0.35980.04571.6437-0.13410.3316-0.0338-0.0324-0.0212-0.11630.03580.01830.03030.0414-0.00210.0899-0.01050.01490.1078-0.00140.08590.47345.426616.84
50.1266-0.1564-0.05141.1373-0.70961.16190.0408-0.0402-0.0392-0.08630.04890.2069-0.2583-0.0625-0.08970.16920.0104-0.00340.0905-0.00310.1357-7.634218.279718.1283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 19
2X-RAY DIFFRACTION2A20 - 75
3X-RAY DIFFRACTION3A76 - 81
4X-RAY DIFFRACTION4A82 - 126
5X-RAY DIFFRACTION5A127 - 154

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