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- PDB-3vu0: Crystal structure of the C-terminal globular domain of oligosacch... -

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Basic information

Entry
Database: PDB / ID: 3vu0
TitleCrystal structure of the C-terminal globular domain of oligosaccharyltransferase (AfAglB-S2, AF_0040, O30195_ARCFU) from Archaeoglobus fulgidus
ComponentsPutative uncharacterized protein
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
Rossmann fold - #12610 / 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 2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,2766
Polymers58,6903
Non-polymers5863
Water6,612367
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7592
Polymers19,5631
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7592
Polymers19,5631
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7592
Polymers19,5631
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.208, 111.208, 36.709
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Putative uncharacterized protein / oligosaccharyltransferase AglB


Mass: 19563.354 Da / Num. of mol.: 3 / Fragment: C-terminal globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AglB / Plasmid: pET-41b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O30195, EC: 2.4.1.119
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10%(w/v) PEG3350, 0.1M magnesium chloride, 0.1M MES-NaOH, pH 6.0, 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: 0.9788 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: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 37597 / Num. obs: 37593 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.5
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1817 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VGP

3vgp


Resolution: 1.94→36.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100803.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3663 10 %RANDOM
Rwork0.188 ---
all0.191 37597 --
obs0.188 36515 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1107 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2---1.24 Å20 Å2
3---2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.94→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 36 367 4247
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.622
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 631 10.9 %
Rwork0.198 5175 -
obs-5806 92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4mes.parammes.top

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