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- PDB-2zai: Crystal structure of the soluble domain of STT3 from P. furiosus -

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Basic information

Entry
Database: PDB / ID: 2zai
TitleCrystal structure of the 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 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)224,20712
Polymers223,9044
Non-polymers3028
Water61334
1
A: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0523
Polymers55,9761
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0523
Polymers55,9761
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oligosaccharyl transferase stt3 subunit related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0523
Polymers55,9761
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)56,0523
Polymers55,9761
Non-polymers762
Water181
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)112,1036
Polymers111,9522
Non-polymers1514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 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)112,1036
Polymers111,9522
Non-polymers1514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.935, 265.297, 74.138
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: 55976.117 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
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: 0.96419 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: 0.96419 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 75298 / Num. obs: 75226 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7371 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZAG
Resolution: 2.7→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
Rfree0.2727 3805 -RANDOM
Rwork0.2271 ---
all-74943 --
obs-74896 99.9 %-
Displacement parametersBiso mean: 44.15 Å2
Baniso -1Baniso -2Baniso -3
1--12.402 Å20 Å20 Å2
2---3.015 Å20 Å2
3---15.416 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14963 0 8 34 15005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3874
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_dihedral_angle_d25.695
X-RAY DIFFRACTIONc_improper_angle_d0.80558
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.3971 381 -
Rwork0.3515 --
obs-7346 99.51 %

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