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- PDB-2zag: Crystal structure of the SeMet-substituted soluble domain of STT3... -

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Basic information

Entry
Database: PDB / ID: 2zag
TitleCrystal structure of the SeMet-substituted soluble domain of STT3 from P. furiosus
ComponentsOligosaccharyl transferase stt3 subunit related protein
KeywordsTRANSFERASE / Multi-domain proteins (alpha and beta)
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / protein glycosylation / metal ion binding / plasma membrane
Similarity search - Function
: / Oligosaccharyl transferase, Peripheral 1 domain / 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, Peripheral 1 domain / 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 furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsMaita, N.
CitationJournal: Embo J. / Year: 2008
Title: Structure-guided identification of a new catalytic motif of oligosaccharyltransferase
Authors: Igura, M. / Maita, N. / Kamishikiryo, J. / Yamada, M. / Obita, T. / Maenaka, K. / Kohda, D.
History
DepositionOct 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligosaccharyl transferase stt3 subunit related protein
B: Oligosaccharyl transferase stt3 subunit related protein
C: Oligosaccharyl transferase stt3 subunit related protein
D: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,14412
Polymers224,8424
Non-polymers3028
Water0
1
A: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2863
Polymers56,2111
Non-polymers762
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2863
Polymers56,2111
Non-polymers762
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2863
Polymers56,2111
Non-polymers762
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2863
Polymers56,2111
Non-polymers762
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Oligosaccharyl transferase stt3 subunit related protein
B: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5726
Polymers112,4212
Non-polymers1514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
MethodPISA
6
C: Oligosaccharyl transferase stt3 subunit related protein
D: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5726
Polymers112,4212
Non-polymers1514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.402, 266.397, 73.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Oligosaccharyl transferase stt3 subunit related protein


Mass: 56210.590 Da / Num. of mol.: 4 / Fragment: Soluble domain, UNP residues 471-967
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF0156 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8U4D2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

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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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 22% PEG 4000, 0.3M NaCOOH, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2005 / Details: mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 55387 / Num. obs: 55387 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5441 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 3916 -RANDOM
Rwork0.2197 ---
all-55142 --
obs-55126 99.99 %-
Displacement parametersBiso mean: 48.64 Å2
Baniso -1Baniso -2Baniso -3
1--4.085 Å20 Å20 Å2
2---4.221 Å20 Å2
3---8.306 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15171 0 8 0 15179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008244
X-RAY DIFFRACTIONc_angle_deg1.50252
X-RAY DIFFRACTIONc_dihedral_angle_d26.01976
X-RAY DIFFRACTIONc_improper_angle_d0.85551
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0.4086 369 -
Rwork0.3572 --
obs-5423 99.76 %

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