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- PDB-9auq: Crystal structure of 4-Fluoro-tryptophan labeled Oscillatoria Aga... -

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Basic information

Entry
Database: PDB / ID: 9auq
TitleCrystal structure of 4-Fluoro-tryptophan labeled Oscillatoria Agardhii agglutinin
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Beta Barrel / carbohydrate binding / fluorinated
Function / homologyOAA-family lectin sugar binding domain / : / OAA-family lectin sugar binding domain / carbohydrate binding / Lectin
Function and homology information
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsRunge, B.R. / Zadorozhnyi, R.R. / Quinn, C.M. / Russell, R.W. / Lu, M. / Antolinez, S. / Struppe, J. / Schwieters, C.D. / Byeon, I.L. / Hadden-Perilla, J. ...Runge, B.R. / Zadorozhnyi, R.R. / Quinn, C.M. / Russell, R.W. / Lu, M. / Antolinez, S. / Struppe, J. / Schwieters, C.D. / Byeon, I.L. / Hadden-Perilla, J. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1708773 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U54AI170791 United States
National Science Foundation (NSF, United States)CHE0959496 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Integrating 19 F Distance Restraints for Accurate Protein Structure Determination by Magic Angle Spinning NMR Spectroscopy.
Authors: Runge, B.R. / Zadorozhnyi, R. / Quinn, C.M. / Russell, R.W. / Lu, M. / Antolinez, S. / Struppe, J. / Schwieters, C.D. / Byeon, I.L. / Hadden-Perilla, J.A. / Gronenborn, A.M. / Polenova, T.
History
DepositionFeb 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9636
Polymers28,0772
Non-polymers8854
Water1,802100
1
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4813
Polymers14,0391
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4813
Polymers14,0391
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.480, 47.303, 47.282
Angle α, β, γ (deg.)78.440, 63.360, 63.370
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lectin


Mass: 14038.704 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planktothrix agardhii (bacteria) / Gene: OAA, NO365_04266 / Production host: Escherichia coli (E. coli) / References: UniProt: C0STD7
#2: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, 0.1 M CAPS (pH 10.5)

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 24, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.37→42.29 Å / Num. obs: 11304 / % possible obs: 95 % / Redundancy: 1.93 % / Rmerge(I) obs: 0.014 / Rrim(I) all: 0.02 / Χ2: 1.22 / Net I/av σ(I): 43.9 / Net I/σ(I): 28.1
Reflection shellResolution: 2.37→2.45 Å / Rmerge(I) obs: 0.025 / Num. unique obs: 1106 / Rrim(I) all: 0.035 / Χ2: 1.06

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→29.9 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1134 10.04 %
Rwork0.1652 10165 -
obs0.1725 11299 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.48 Å2 / Biso mean: 14.337 Å2 / Biso min: 2.62 Å2
Refinement stepCycle: final / Resolution: 2.37→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 56 100 2134
Biso mean--18.98 15.3 -
Num. residues----264
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.480.23420.16251181X-RAY DIFFRACTION89
2.48-2.610.32960.20161236X-RAY DIFFRACTION95
2.61-2.770.33430.19941265X-RAY DIFFRACTION95
2.77-2.990.25390.20561302X-RAY DIFFRACTION96
2.99-3.290.24040.19781269X-RAY DIFFRACTION96
3.29-3.760.2420.14891316X-RAY DIFFRACTION97
3.76-4.730.16590.13041317X-RAY DIFFRACTION96
4.74-29.90.21510.1371279X-RAY DIFFRACTION96

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