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- PDB-3waj: Crystal structure of the Archaeoglobus fulgidus oligosaccharyltra... -

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Basic information

Entry
Database: PDB / ID: 3waj
TitleCrystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) complex with Zn and sulfate
ComponentsTransmembrane oligosaccharyl transferase
KeywordsTRANSFERASE / oligosaccharyltransferase / N-glycosylation / Archaeoglobus fulgidus / GT-C / protein b-oligosaccharyltransferase
Function / homology
Function and homology information


dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / protein glycosylation / metal ion binding / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1650 / Immunoglobulin-like - #3390 / Oligosaccharyl transferase, archaeal / Archaeal glycosylation protein B, peripheral domain / Archaeal glycosylation protein B long peripheral domain / Rossmann fold - #12610 / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1650 / Immunoglobulin-like - #3390 / Oligosaccharyl transferase, archaeal / Archaeal glycosylation protein B, peripheral domain / Archaeal glycosylation protein B long peripheral domain / Rossmann fold - #12610 / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Dolichyl-phosphooligosaccharide-protein glycotransferase 3
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsMatsumoto, S. / Shimada, A. / Kohda, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation
Authors: Matsumoto, S. / Shimada, A. / Nyirenda, J. / Igura, M. / Kawano, Y. / Kohda, D.
History
DepositionMay 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 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_asym_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_asym_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_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_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: Transmembrane oligosaccharyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2753
Polymers99,1141
Non-polymers1612
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)234.195, 108.961, 56.069
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transmembrane oligosaccharyl transferase / AfAglB-L


Mass: 99113.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: aglB-L / Plasmid: pET52b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: O29867, EC: 2.4.1.119
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M zinc sulfate, 0.1M sodium acetate buffer, 15% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→38.813 Å / Num. all: 47863 / Num. obs: 47863 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2369 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WAI

3wai


Resolution: 2.501→38.813 Å / Occupancy max: 2.25 / Occupancy min: 1 / FOM work R set: 0.8573 / SU ML: 0.23 / σ(F): 1.43 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 2382 5.08 %random
Rwork0.1825 ---
all0.1842 47863 --
obs0.1842 46879 96.77 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.37 Å2 / Biso mean: 56.31 Å2 / Biso min: 17.6 Å2
Refinement stepCycle: LAST / Resolution: 2.501→38.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6368 0 6 151 6525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086577
X-RAY DIFFRACTIONf_angle_d1.158976
X-RAY DIFFRACTIONf_chiral_restr0.083972
X-RAY DIFFRACTIONf_plane_restr0.0061118
X-RAY DIFFRACTIONf_dihedral_angle_d14.8622266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5012-2.55220.28471410.23652398253988
2.5522-2.60770.26871430.22882485262893
2.6077-2.66830.28451250.22042571269694
2.6683-2.7350.2481440.21082505264995
2.735-2.8090.2281290.19232648277796
2.809-2.89160.23791340.19432531266596
2.8916-2.98490.23331400.18852627276797
2.9849-3.09150.20571320.18332636276897
3.0915-3.21530.23091440.1852627277198
3.2153-3.36150.241390.18182651279099
3.3615-3.53860.21381550.18282676283199
3.5386-3.76020.22321490.17172668281799
3.7602-4.05020.23721260.16692696282299
4.0502-4.45730.17211340.15532686282099
4.4573-5.1010.18611600.15832710287099
5.101-6.4220.22281450.192527022847100
6.422-38.81740.20181420.20142680282297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.26570.11280.19230.5664-0.0580.92920.4241-0.1899-0.17830.2106-0.1189-0.11370.2223-0.05680.47890.3263-0.0557-0.19340.2080.07010.223-37.7202-19.264230.0941
20.8365-0.18310.15330.1670.13370.51970.4459-0.2526-0.08540.3257-0.1535-0.07010.3508-0.31130.06190.4293-0.27440.00270.37890.05170.2682-59.4752-26.5925.2001
30.1587-0.08130.14620.1527-0.06360.13940.2440.31140.0412-0.06150.11290.16760.05330.05160.03410.4706-0.13090.08230.48790.01290.4006-73.1127-35.530713.0211
40.3046-0.2189-0.33120.15730.23970.36230.2370.3396-0.7168-0.23050.073-0.57690.19360.12560.29430.52990.0515-0.21060.2485-0.16990.9135-37.5556-39.178516.8029
51.48330.88930.63420.64560.4781.29390.13520.1040.01990.0557-0.06230.0082-0.05940.0320.010.21010.03960.05530.1881-0.01790.1986-33.63343.930716.9666
60.5181-0.0389-0.28250.0876-0.00320.38760.10470.09090.11050.00480.0374-0.0512-0.03510.1581-00.2321-0.0090.01450.3728-0.00170.3168-12.1303-1.42962.6801
70.33310.0972-0.21390.27680.01870.14890.1985-0.12080.42970.06090.0005-0.1781-0.35560.25330.0920.476-0.10630.15830.2706-0.01750.5374-16.300522.693611.284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 15:182)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 183:295)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 296:333)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 374:494)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 495:634)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 635:760)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 761:868)

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