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- PDB-9c1a: Crystal structure of GDP-bound human M-RAS protein in crystal form I -

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Basic information

Entry
Database: PDB / ID: 9c1a
TitleCrystal structure of GDP-bound human M-RAS protein in crystal form I
ComponentsRas-related protein M-Ras
KeywordsHYDROLASE / M-RAS / GDP / GTPase structure / RAS / crystal packing
Function / homology
Function and homology information


protein phosphatase type 1 complex / GTP-dependent protein binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / cellular response to leukemia inhibitory factor / small monomeric GTPase / RAF activation / GDP binding / G protein activity / actin cytoskeleton organization ...protein phosphatase type 1 complex / GTP-dependent protein binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / cellular response to leukemia inhibitory factor / small monomeric GTPase / RAF activation / GDP binding / G protein activity / actin cytoskeleton organization / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein M-Ras
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBester, S.M. / Abrahamsen, R. / Samora, L.R. / Wu, W.-I. / Mou, T.-C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystal structure of the GDP-bound human M-RAS protein in two crystal forms.
Authors: Bester, S.M. / Abrahamsen, R. / Rodrigues Samora, L. / Wu, W.I. / Mou, T.C.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein M-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0217
Polymers22,2531
Non-polymers7686
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.653, 108.653, 65.759
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-369-

HOH

21A-490-

HOH

31A-500-

HOH

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Components

#1: Protein Ras-related protein M-Ras / Ras-related protein R-Ras3


Mass: 22253.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRAS, RRAS3 / Production host: Escherichia coli (E. coli) / References: UniProt: O14807, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M CaCl2, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→54.33 Å / Num. obs: 16016 / % possible obs: 94.03 % / Redundancy: 38.3 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 1 / Rpim(I) all: 0.032 / Rrim(I) all: 0.202 / Net I/σ(I): 19.82
Reflection shellResolution: 1.96→2.03 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1643 / CC1/2: 0.943 / Rpim(I) all: 0.293 / Rrim(I) all: 1.732 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→54.33 Å / SU ML: 0.2004 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 1601 10 %
Rwork0.1718 14415 -
obs0.1747 16016 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.97 Å2
Refinement stepCycle: LAST / Resolution: 1.96→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 48 217 1623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451443
X-RAY DIFFRACTIONf_angle_d0.87621954
X-RAY DIFFRACTIONf_chiral_restr0.0512215
X-RAY DIFFRACTIONf_plane_restr0.0054245
X-RAY DIFFRACTIONf_dihedral_angle_d15.6455202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.020.27631490.21141345X-RAY DIFFRACTION99.87
2.02-2.090.2341060.2027959X-RAY DIFFRACTION70.16
2.09-2.180.22741500.17121350X-RAY DIFFRACTION99.93
2.18-2.280.21341210.18221088X-RAY DIFFRACTION78.97
2.28-2.40.20481520.16461368X-RAY DIFFRACTION100
2.4-2.550.21421530.16861378X-RAY DIFFRACTION99.93
2.55-2.740.21251380.17581238X-RAY DIFFRACTION89.76
2.74-3.020.20091540.16341387X-RAY DIFFRACTION99.94
3.02-3.450.17161560.15751400X-RAY DIFFRACTION100
3.45-4.350.16731520.14121371X-RAY DIFFRACTION95.97
4.35-54.330.2121700.20011531X-RAY DIFFRACTION99.53

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