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

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Basic information

Entry
Database: PDB / ID: 3vgp
TitleCrystal structure of the C-terminal globular domain of oligosaccharyltransferase (AF_0329) from Archaeoglobus fulgidus
ComponentsTransmembrane oligosaccharyl transferase, putative
KeywordsTRANSFERASE / glycosyltransferase / cell membrane
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / : / metal ion binding / plasma membrane
Similarity search - Function
Rossmann fold - #12610 / : / AglB core domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dolichyl-phosphooligosaccharide-protein glycotransferase 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsMatsumoto, S. / Igura, M. / Nyirenda, J. / Yuzawa, S. / Noda, N.N. / Inagaki, F. / Kohda, D.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal Structure of the C-Terminal Globular Domain of Oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 A Resolution
Authors: Matsumoto, S. / Igura, M. / Nyirenda, J. / Matsumoto, M. / Yuzawa, S. / Noda, N.N. / Inagaki, F. / Kohda, D.
History
DepositionAug 18, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane oligosaccharyl transferase, putative


Theoretical massNumber of molelcules
Total (without water)19,2931
Polymers19,2931
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.046, 47.046, 159.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transmembrane oligosaccharyl transferase, putative


Mass: 19292.887 Da / Num. of mol.: 1 / Fragment: C-terminal globular domain / Mutation: C482A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0329 / Plasmid: pET-47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: O29918, EC: 2.4.1.119
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12.5% PEG 3350, 0.1M bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9798 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 22, 2010
RadiationMonochromator: a double-crystal monochromator and a horizontal focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 19197 / Num. obs: 18986 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 27 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 98.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 24.8 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 13 / Num. unique all: 853 / % possible all: 93.9

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→40.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 234062.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1838 9.9 %RANDOM
Rwork0.223 ---
all0.226 19016 --
obs0.223 18598 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.7233 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--1.54 Å20 Å2
3----3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.75→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 0 154 1455
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it3.52.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 268 9.2 %
Rwork0.24 2654 -
obs-2922 95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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