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- PDB-6oyc: Glycosylation Associate Protein (Gap123) complex from Streptococc... -

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Basic information

Entry
Database: PDB / ID: 6oyc
TitleGlycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae
Components(Glycosylation Associate Protein ...) x 3
KeywordsSUGAR BINDING PROTEIN / Glycosylation / Secretion / lectin
Function / homology
Function and homology information


Accessory Sec system protein Asp2 / Accessory Sec system GspB-transporter / Accessory Sec system protein Asp3 / Accessory Sec secretory system ASP3 / Accessory secretory system protein Asp1 / Accessory Sec system protein Asp1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Accessory secretory protein Asp1 / Accessory Sec system protein Asp2 / Conserved domain protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serotype V
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.351 Å
Authorszhang, H. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5R01DE017954-12 United States
CitationJournal: To Be Published
Title: Glycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae
Authors: zhang, H. / Zhu, F. / Wu, H.
History
DepositionMay 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosylation Associate Protein 1
B: Glycosylation Associate Protein 2
C: Glycosylation Associate Protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,20619
Polymers157,7213
Non-polymers1,48516
Water7,260403
1
A: Glycosylation Associate Protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2869
Polymers60,5411
Non-polymers7458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosylation Associate Protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7166
Polymers59,2521
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycosylation Associate Protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2044
Polymers37,9281
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-72 kcal/mol
Surface area53650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.009, 168.321, 100.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-552-

HOH

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Components

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Glycosylation Associate Protein ... , 3 types, 3 molecules ABC

#1: Protein Glycosylation Associate Protein 1


Mass: 60541.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R) (bacteria)
Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1452 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DYM4
#2: Protein Glycosylation Associate Protein 2


Mass: 59251.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R) (bacteria)
Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1451 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DYM5
#3: Protein Glycosylation Associate Protein 3


Mass: 37928.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R) (bacteria)
Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DYM6

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Non-polymers , 3 types, 419 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 5% PEG 400, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→49.272 Å / Num. obs: 72701 / % possible obs: 99.55 % / Redundancy: 14.1 % / Net I/σ(I): 28.13
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 7084

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Processing

Software
NameVersionClassification
PHENIX(dev_3051: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E2I

6e2i
PDB Unreleased entry


Resolution: 2.351→49.272 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.21
RfactorNum. reflection% reflection
Rfree0.2267 2000 2.75 %
Rwork0.181 --
obs0.1822 72660 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.351→49.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10827 0 93 403 11323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811159
X-RAY DIFFRACTIONf_angle_d0.92815069
X-RAY DIFFRACTIONf_dihedral_angle_d3.7676605
X-RAY DIFFRACTIONf_chiral_restr0.0541620
X-RAY DIFFRACTIONf_plane_restr0.0051921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3515-2.41030.28481420.22944918X-RAY DIFFRACTION98
2.4103-2.47540.28011340.21744948X-RAY DIFFRACTION99
2.4754-2.54830.29681440.20894958X-RAY DIFFRACTION99
2.5483-2.63050.26921430.20485013X-RAY DIFFRACTION100
2.6305-2.72450.27731480.19914978X-RAY DIFFRACTION100
2.7245-2.83360.25641390.20085018X-RAY DIFFRACTION100
2.8336-2.96250.25671360.20555031X-RAY DIFFRACTION100
2.9625-3.11870.25671460.19865062X-RAY DIFFRACTION100
3.1187-3.31410.26351450.19565020X-RAY DIFFRACTION100
3.3141-3.56990.25721410.18485078X-RAY DIFFRACTION100
3.5699-3.9290.22831430.16965055X-RAY DIFFRACTION100
3.929-4.49720.20081420.14955134X-RAY DIFFRACTION100
4.4972-5.66470.18571480.15575141X-RAY DIFFRACTION100
5.6647-49.28290.17251490.18245306X-RAY DIFFRACTION99

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