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- PDB-3wzt: Crystal structure of Trx3 domain of UGGT (detergent-unbound form) -

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Basic information

Entry
Database: PDB / ID: 3wzt
TitleCrystal structure of Trx3 domain of UGGT (detergent-unbound form)
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / Thioredoxin fold / Endoplasmic reticulum / Quality control / glucosyltransferase / folding sensor / Thioredoxin-like
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein N-linked glycosylation via asparagine / unfolded protein binding / endoplasmic reticulum lumen / nucleotide binding / metal ion binding
Similarity search - Function
UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain ...UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain / Glucosyltransferase 24 / UDP-glucose:Glycoprotein Glucosyltransferase / Nucleotide-diphospho-sugar transferases / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsZhu, T. / Satoh, T. / Kato, K.
CitationJournal: Sci Rep / Year: 2014
Title: Structural insight into substrate recognition by the endoplasmic reticulum folding-sensor enzyme: crystal structure of third thioredoxin-like domain of UDP-glucose:glycoprotein glucosyltransferase
Authors: Zhu, T. / Satoh, T. / Kato, K.
History
DepositionOct 3, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 8, 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_ncs_dom_lim / 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.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose-glycoprotein glucosyltransferase-like protein
B: UDP-glucose-glycoprotein glucosyltransferase-like protein
C: UDP-glucose-glycoprotein glucosyltransferase-like protein
D: UDP-glucose-glycoprotein glucosyltransferase-like protein
E: UDP-glucose-glycoprotein glucosyltransferase-like protein
F: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)110,3416
Polymers110,3416
Non-polymers00
Water0
1
A: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)18,3901
Polymers18,3901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)18,3901
Polymers18,3901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)18,3901
Polymers18,3901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)18,3901
Polymers18,3901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)18,3901
Polymers18,3901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: UDP-glucose-glycoprotein glucosyltransferase-like protein


Theoretical massNumber of molelcules
Total (without water)18,3901
Polymers18,3901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)196.4, 196.4, 196.4
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24F
15B
25C
16B
26D
17B
27F
18C
28D
19C
29F
110D
210F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUAA673 - 8295 - 161
21ASNASNLEULEUBB673 - 8295 - 161
12ASNASNGLNGLNAA679 - 83011 - 162
22ASNASNGLNGLNCC679 - 83011 - 162
13LYSLYSLEULEUAA674 - 8296 - 161
23LYSLYSLEULEUDD674 - 8296 - 161
14THRTHRGLUGLUAA696 - 82628 - 158
24VALVALGLUGLUFF686 - 82618 - 158
15ASNASNGLNGLNBB679 - 83011 - 162
25ASNASNGLNGLNCC679 - 83011 - 162
16LYSLYSLEULEUBB674 - 8296 - 161
26LYSLYSLEULEUDD674 - 8296 - 161
17THRTHRGLUGLUBB696 - 82628 - 158
27VALVALGLUGLUFF686 - 82618 - 158
18ASNASNGLNGLNCC679 - 83011 - 162
28ASNASNGLNGLNDD679 - 83011 - 162
19VALVALVALVALCC686 - 82718 - 159
29VALVALVALVALFF686 - 82718 - 159
110THRTHRGLUGLUDD696 - 82628 - 158
210VALVALGLUGLUFF686 - 82618 - 158

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
UDP-glucose-glycoprotein glucosyltransferase-like protein


Mass: 18390.176 Da / Num. of mol.: 6 / Fragment: Trx3 domain, UNP residues 671-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Plasmid: pCold-GST (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: G0SB58

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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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97888 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97888 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 17447 / Num. obs: 17411 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 44.7 % / Biso Wilson estimate: 81.8 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 34.1
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 45.4 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 6.7 / Num. unique all: 1722 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZS

3wzs


Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.863 / SU B: 28.996 / SU ML: 0.476 / Cross valid method: THROUGHOUT / ESU R Free: 0.634 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 865 5 %RANDOM
Rwork0.235 ---
obs0.237 16478 99.41 %-
all-16478 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.819 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 0 0 6452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196544
X-RAY DIFFRACTIONr_bond_other_d0.0060.026299
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.988830
X-RAY DIFFRACTIONr_angle_other_deg1.041314481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027303
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021436
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.8419.4223226
X-RAY DIFFRACTIONr_mcbond_other7.8359.4213225
X-RAY DIFFRACTIONr_mcangle_it11.99714.1093994
X-RAY DIFFRACTIONr_mcangle_other11.99614.113995
X-RAY DIFFRACTIONr_scbond_it8.62910.293317
X-RAY DIFFRACTIONr_scbond_other8.62810.293318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.84815.14837
X-RAY DIFFRACTIONr_long_range_B_refined18.07197.0185213
X-RAY DIFFRACTIONr_long_range_B_other18.0797.025214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A94850.06
12B94850.06
21A86550.07
22C86550.07
31A94160.06
32D94160.06
41A62740.07
42F62740.07
51B85740.07
52C85740.07
61B93720.06
62D93720.06
71B62800.08
72F62800.08
81C86690.06
82D86690.06
91C66480.06
92F66480.06
101D63470.06
102F63470.06
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 58 -
Rwork0.257 1194 -
obs--100 %

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