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- PDB-3vu1: Crystal structure of the C-terminal globular domain of oligosacch... -

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Basic information

Entry
Database: PDB / ID: 3vu1
TitleCrystal structure of the C-terminal globular domain of oligosaccharyltransferase (PhAglB-L, O74088_PYRHO) from Pyrococcus horikoshii
ComponentsPutative uncharacterized protein PH0242
KeywordsTRANSFERASE / glycotransferase / Asn-glycosylation / membrane
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / protein glycosylation / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Lipocalin - #390 / Immunoglobulin-like - #3020 / Immunoglobulin-like - #3030 / Oligosaccharyltransferase, peripheral 2 domain / Oligosaccharyltransferase insert domain / Oligosaccharyltransferase Peripheral 2 domain / Oligosaccharyltransferase Insert domain / Rossmann fold - #12610 / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal ...Lipocalin - #390 / Immunoglobulin-like - #3020 / Immunoglobulin-like - #3030 / Oligosaccharyltransferase, peripheral 2 domain / Oligosaccharyltransferase insert domain / Oligosaccharyltransferase Peripheral 2 domain / Oligosaccharyltransferase Insert domain / Rossmann fold - #12610 / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Lipocalin / Immunoglobulin-like / Beta Barrel / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Dolichyl-phosphooligosaccharide-protein glycotransferase 1
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNyirenda, J. / Matsumoto, S. / Saitoh, T. / Maita, N. / Noda, N.N. / Inagaki, F. / Kohda, D.
CitationJournal: Structure / Year: 2013
Title: Crystallographic and NMR Evidence for Flexibility in Oligosaccharyltransferases and Its Catalytic Significance
Authors: Nyirenda, J. / Matsumoto, S. / Saitoh, T. / Maita, N. / Noda, N.N. / Inagaki, F. / Kohda, D.
History
DepositionJun 13, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein PH0242
B: Putative uncharacterized protein PH0242
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2726
Polymers115,1212
Non-polymers1514
Water1,44180
1
A: Putative uncharacterized protein PH0242
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6363
Polymers57,5611
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein PH0242
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6363
Polymers57,5611
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-12 kcal/mol
Surface area45120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.467, 94.844, 186.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein PH0242 / oligosaccharyltransferase AglB


Mass: 57560.605 Da / Num. of mol.: 2 / Fragment: C-terminal globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: AGLB / Plasmid: pET-41b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O74088, EC: 2.4.1.119
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15%(w/v) PEG3350, 0.2M sodium citrate, 0.1M bis-Tris propane-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2010
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 41938 / Num. obs: 41657 / % possible obs: 99.33 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.81
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4 / Num. unique all: 2020 / % possible all: 89.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZAG

2zag


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.128 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.491 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21469 2071 5 %RANDOM
Rwork0.17131 ---
obs0.1735 41143 99.33 %-
all-41419 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.724 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20 Å2
2--0.87 Å20 Å2
3----2.73 Å2
Refine analyzeLuzzati sigma a obs: 0.298 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7843 0 4 80 7927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028050
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.95310909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38923.26365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.918151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9421552
X-RAY DIFFRACTIONr_chiral_restr0.0990.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216096
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 146 -
Rwork0.269 2605 -
obs-2605 98.32 %

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