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- PDB-9ewk: Solvent organization in ultrahigh-resolution protein crystal stru... -

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Basic information

Entry
Database: PDB / ID: 9ewk
TitleSolvent organization in ultrahigh-resolution protein crystal structure at room temperature
ComponentsCrambin
KeywordsPLANT PROTEIN / Crambin
Function / homologyThionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / defense response / extracellular region / ETHANOL / Crambin
Function and homology information
Biological speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.7 Å
AuthorsChen, J.C.-H. / Gilski, M. / Chang, C. / Borek, D. / Rosenbaum, G. / Lavens, A. / Otwinowski, Z. / Kubicki, M. / Dauter, Z. / Jaskolski, M. / Joachimiak, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35GM145365 United States
CitationJournal: Iucrj / Year: 2024
Title: Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature.
Authors: Chen, J.C.H. / Gilski, M. / Chang, C. / Borek, D. / Rosenbaum, G. / Lavens, A. / Otwinowski, Z. / Kubicki, M. / Dauter, Z. / Jaskolski, M. / Joachimiak, A.
History
DepositionApr 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crambin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8213
Polymers4,7281
Non-polymers922
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint3 kcal/mol
Surface area3140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.725, 18.767, 41.059
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Crambin


Mass: 4728.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Natural mixture of the two isoform PL/SI
Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
References: UniProt: P01542
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.83 Å3/Da / Density % sol: 32.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 80% (v/v) ethanol:water solution

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.39995 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.39995 Å / Relative weight: 1
ReflectionResolution: 0.7→14.47 Å / Num. obs: 54039 / % possible obs: 98.2 % / Redundancy: 13.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.013 / Rrim(I) all: 0.05 / Χ2: 0.971 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
0.7-0.7114.32.21813200.620.8750.5962.2970.96499
0.71-0.7114.11.83113530.670.8960.4951.8970.96798.9
0.71-0.7214.31.82413770.6640.8930.4921.890.97199.3
0.72-0.7314.11.62813500.7680.9320.441.6880.97998.8
0.73-0.7314.21.39913640.7940.9410.3791.450.97199
0.73-0.7414.11.30913210.8210.950.3561.3570.95199
0.74-0.7514.21.27213510.7980.9420.3451.3190.97498.7
0.75-0.7514.11.09113690.8460.9570.2961.1310.98598.8
0.75-0.7614.11.03113270.8730.9650.281.069199
0.76-0.7714.10.95313500.8930.9710.2580.9880.99998.8
0.77-0.7813.90.89613670.8950.9720.2450.9290.98798.7
0.78-0.7913.90.8113360.9080.9760.2220.8411.01998.7
0.79-0.813.90.77113320.9190.9790.2110.80.98998.2
0.8-0.8113.90.67613560.9340.9830.1850.7021.00499.1
0.81-0.8213.90.62813950.9430.9850.1720.6521.00499.4
0.82-0.8313.80.55413090.9540.9880.1520.5750.99998.9
0.83-0.8413.60.4914000.9640.9910.1350.5091.01898.7
0.84-0.8513.70.43113120.9710.9930.1190.4481.01798.9
0.85-0.8713.30.38613600.9740.9940.1090.4011.0298.6
0.87-0.8812.90.34313450.980.9950.0980.3571.01798.5
0.88-0.912.50.30913530.980.9950.090.3221.03398.4
0.9-0.9112.20.26413170.9820.9960.0780.2761.02796.4
0.91-0.9311.50.20512240.9880.9970.0630.2151.03690.3
0.93-0.9511.90.18212910.9910.9980.0550.191.04392.7
0.95-0.9713.60.15713120.9950.9990.0440.1631.01498.4
0.97-0.9914.50.13514130.9970.9990.0360.141.01199
0.99-1.0214.40.11313430.9970.9990.0310.1170.98499.3
1.02-1.0514.40.09813690.9970.9990.0260.1020.98998.7
1.05-1.0814.30.08213440.99810.0220.0851.00299.3
1.08-1.1114.30.07313720.99810.020.0760.98999.3
1.11-1.1514.30.06213740.99910.0170.0640.97499.6
1.15-1.2140.05713790.99910.0150.0590.95499.7
1.2-1.2514.10.05213700.99910.0140.0530.94699.4
1.25-1.3213.80.04713660.99910.0130.0480.999.3
1.32-1.413.50.04113910.99910.0110.0430.8899.3
1.4-1.5113.30.03513710.99910.010.0360.84698.8
1.51-1.6612.50.02913530.99910.0080.030.80697.6
1.66-1.912.30.02412350.99910.0070.0250.7887.4
1.9-2.39150.0211406110.0050.0210.79100
2.39-100140.02114620.99910.0060.0210.99599.3

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Processing

Software
NameClassification
SHELXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.7→14.47 Å / Cross valid method: NONE
Details: The hydrogen atoms were added and refined at riding positions. Anisotropic atomic displacement parameters were used. The final refinement was calculated using weighted full-matrix least- ...Details: The hydrogen atoms were added and refined at riding positions. Anisotropic atomic displacement parameters were used. The final refinement was calculated using weighted full-matrix least-squares procedure. There were no geometric restraints for ordered protein fragments.
RfactorNum. reflection% reflection
Rwork0.0759 --
obs-47117 83.1 %
Displacement parametersBiso mean: 5.059 Å2
Refinement stepCycle: LAST / Resolution: 0.7→14.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms341 0 6 57 404

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