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- PDB-7lt8: Crystal structure of Ras suppressor-1 -

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Basic information

Entry
Database: PDB / ID: 7lt8
TitleCrystal structure of Ras suppressor-1
ComponentsRas suppressor protein 1
KeywordsCELL ADHESION / leucine-rich repeat
Function / homology
Function and homology information


Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of cell-substrate adhesion / positive regulation of GTPase activity / focal adhesion / signal transduction / extracellular exosome / cytosol
Similarity search - Function
Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Ras suppressor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76000247097 Å
AuthorsFukuda, K. / Qin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular basis for Ras suppressor-1 binding to PINCH-1 in focal adhesion assembly.
Authors: Fukuda, K. / Lu, F. / Qin, J.
History
DepositionFeb 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 6, 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: Ras suppressor protein 1


Theoretical massNumber of molelcules
Total (without water)31,8621
Polymers31,8621
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.851, 45.328, 83.052
Angle α, β, γ (deg.)90.000, 99.024, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Ras suppressor protein 1 / RSP-1 / Rsu-1


Mass: 31861.537 Da / Num. of mol.: 1 / Fragment: Leucine-rich repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RSU1, RSP1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf-9 / References: UniProt: Q15404
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.86 Å3/Da / Density % sol: 33.81 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8.5 / Details: PEG4000, lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 22975 / % possible obs: 97.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 22.2947677536 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 36.52
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 1136

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.10_2155refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76000247097→27.3413475696 Å / SU ML: 0.161477691195 / Cross valid method: THROUGHOUT / σ(F): 1.34364813708 / Phase error: 22.0795682201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.216659361064 1178 5.1816662268 %RANDOM
Rwork0.173273824954 21556 --
obs0.175516614945 22734 97.1621506112 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.430761098 Å2
Refinement stepCycle: LAST / Resolution: 1.76000247097→27.3413475696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 0 131 2139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006107416893162046
X-RAY DIFFRACTIONf_angle_d0.8143322086582774
X-RAY DIFFRACTIONf_chiral_restr0.051426303141321
X-RAY DIFFRACTIONf_plane_restr0.00592777606187360
X-RAY DIFFRACTIONf_dihedral_angle_d17.46590488051258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76000247097-1.84010.2478431954171520.2037268463362624X-RAY DIFFRACTION96.3888888889
1.8401-1.93710.2170738905721500.1933150181832654X-RAY DIFFRACTION96.6896551724
1.9371-2.05840.2359277165691590.17496441952672X-RAY DIFFRACTION96.7532467532
2.0584-2.21730.2397403544941620.1654710050412657X-RAY DIFFRACTION97.2404277337
2.2173-2.44030.2277368800961290.1688374368792704X-RAY DIFFRACTION96.9541409993
2.4403-2.79310.2528707061311280.1852436127162739X-RAY DIFFRACTION98.2185680027
2.7931-3.51780.2360620845131310.184546042482762X-RAY DIFFRACTION98.0677966102

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