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- PDB-3pit: Crystal structure of M-RasD41E in complex with GppNHp (type 2) -

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Basic information

Entry
Database: PDB / ID: 3pit
TitleCrystal structure of M-RasD41E in complex with GppNHp (type 2)
ComponentsRas-related protein M-Ras
KeywordsSIGNALING PROTEIN / GTP-binding / GTPase
Function / homology
Function and homology information


RAF activation / GTP-dependent protein binding / cellular response to leukemia inhibitory factor / small monomeric GTPase / G protein activity / GDP binding / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family 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 nucleotide triphosphate hydrolases ...Small GTPase, Ras-type / small GTPase Ras family 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein M-Ras
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMuraoka, S. / Matsumoto, K. / Shima, F. / Hu, L. / Ijiri, Y. / Hirai, R. / Liao, J. / Kataoka, T.
CitationJournal: To be Published
Title: Crystal structure of M-RasD41E in complex with GppNHp (type 2)
Authors: Muraoka, S. / Matsumoto, K. / Shima, F. / Hu, L. / Ijiri, Y. / Hirai, R. / Liao, J. / Kataoka, T.
History
DepositionNov 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)21,3973
Polymers20,8511
Non-polymers5472
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.111, 89.646, 41.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Ras-related protein M-Ras / Muscle and microspikes Ras / Ras-related protein R-Ras3 / X-Ras


Mass: 20850.758 Da / Num. of mol.: 1 / Fragment: G domain, UNP residues 1-178 / Mutation: D41E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mras, Xras / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08989
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Tris-HCl, 0.2M magnesium chloride, 25% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→18.6 Å / Num. all: 25878 / Num. obs: 25878 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.4
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3685 / Rsym value: 0.283 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X1S

1x1s


Resolution: 1.55→15.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.327 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21271 1313 5.1 %RANDOM
Rwork0.18469 ---
all0.18617 24516 --
obs0.18617 24516 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.466 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 33 159 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221507
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9912059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1424.16772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2621510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211149
X-RAY DIFFRACTIONr_mcbond_it0.6591.5887
X-RAY DIFFRACTIONr_mcangle_it1.24221460
X-RAY DIFFRACTIONr_scbond_it1.9083620
X-RAY DIFFRACTIONr_scangle_it3.0594.5599
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 74 -
Rwork0.224 1780 -
obs-1780 97.32 %

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