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- PDB-3ggy: Crystal Structure of S.cerevisiae Ist1 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3ggy
TitleCrystal Structure of S.cerevisiae Ist1 N-terminal domain
ComponentsIncreased sodium tolerance protein 1
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS / ESCRT-III like / Phosphoprotein
Function / homology
Function and homology information


Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to vacuole transport via multivesicular body sorting pathway / endosome to plasma membrane protein transport / ATPase inhibitor activity / Neutrophil degranulation / intracellular protein localization / endosome / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein IST1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsXiao, J. / Xu, Z.
CitationJournal: MOLECULAR BIOLOGY OF THE CELL / Year: 2009
Title: Structural basis of Ist1 function and Ist1-Did2 interaction in the multivesicular body pathway and cytokinesis.
Authors: Xiao, J. / Chen, X.W. / Davies, B.A. / Saltiel, A.R. / Katzmann, D.J. / Xu, Z.
History
DepositionMar 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Increased sodium tolerance protein 1
B: Increased sodium tolerance protein 1


Theoretical massNumber of molelcules
Total (without water)44,7602
Polymers44,7602
Non-polymers00
Water8,143452
1
A: Increased sodium tolerance protein 1


Theoretical massNumber of molelcules
Total (without water)22,3801
Polymers22,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Increased sodium tolerance protein 1


Theoretical massNumber of molelcules
Total (without water)22,3801
Polymers22,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.845, 44.172, 66.952
Angle α, β, γ (deg.)90.000, 110.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Increased sodium tolerance protein 1


Mass: 22380.164 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 1-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IST1, N0809, YNL265C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53843
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: PEG 3000, NaAc, MgCl2, Glycine, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9793 Å
DetectorDetector: CCD / Date: Apr 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 30.26 / Number: 121168 / Rmerge(I) obs: 0.061 / Χ2: 1.09 / D res high: 2.85 Å / D res low: 50 Å / Num. obs: 19282 / % possible obs: 96.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.735091.810.0343.0566
6.147.7394.710.0471.2776.4
5.366.1495.410.0511.236.4
4.875.3695.710.0431.2066.4
4.524.8795.910.0421.2026.3
4.264.5295.810.0441.3736.3
4.044.2696.810.051.1136.4
3.874.0496.910.0551.1096.4
3.723.8797.410.0621.0466.3
3.593.729710.0731.026.3
3.483.5997.710.081.0286.3
3.383.4897.510.090.9546.3
3.293.389810.0970.8666.3
3.213.299810.1070.8066.3
3.143.2198.310.1190.8086.2
3.073.1498.110.1320.7776.3
3.013.0798.410.1330.7436.2
2.953.0198.210.1540.7436.3
2.92.9598.610.1570.7426.1
2.852.998.910.1770.6866.2
ReflectionResolution: 1.7→50 Å / Num. obs: 43548 / % possible obs: 98.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 / Χ2: 1.014 / Net I/σ(I): 30.261
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.733.40.20420760.67195.1
1.73-1.763.50.19521050.68295.8
1.76-1.793.60.17821130.70498.2
1.79-1.833.70.16121800.75298.6
1.83-1.873.80.14521400.75798.8
1.87-1.913.80.13122030.76398.9
1.91-1.963.80.11721400.79599.4
1.96-2.023.80.10121850.91298.7
2.02-2.073.80.08721481.002100
2.07-2.143.80.07721731.04299
2.14-2.223.80.06621951.05799.3
2.22-2.313.80.0622011.072100
2.31-2.413.80.05321821.06299.5
2.41-2.543.80.04721820.99799.7
2.54-2.73.80.04722061.15699.8
2.7-2.913.80.04922131.44499.9
2.91-3.23.80.0422031.37799.7
3.2-3.663.70.03222181.42999.8
3.66-4.613.70.02422111.38499
4.61-503.60.02622741.07498.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
SHARPphasing
RefinementResolution: 1.7→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.822 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.249 2158 4.9 %
Rwork0.226 --
obs-43503 98.9 %
Solvent computationBsol: 49.512 Å2
Displacement parametersBiso max: 58.64 Å2 / Biso mean: 23.471 Å2 / Biso min: 5.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.052 Å20 Å2-5.29 Å2
2--0.21 Å20 Å2
3---2.842 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 0 452 3492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.971
X-RAY DIFFRACTIONc_mcbond_it1.2861.5
X-RAY DIFFRACTIONc_scbond_it2.4622
X-RAY DIFFRACTIONc_mcangle_it1.9392
X-RAY DIFFRACTIONc_scangle_it3.8112.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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