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- PDB-1lxd: CRYSTAL STRUCTURE OF THE RAS INTERACTING DOMAIN OF RALGDS, A GUAN... -

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Basic information

Entry
Database: PDB / ID: 1lxd
TitleCRYSTAL STRUCTURE OF THE RAS INTERACTING DOMAIN OF RALGDS, A GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR OF RAL PROTEIN
ComponentsRALGDSB
KeywordsPHOSPHORYLATION / RALGDS / RAS BINDING / UBIQUITIN FOLD / CDC25 FAMILY / SIGNAL TRANSDUCTION / CROSS-TALK
Function / homology
Function and homology information


p38MAPK events / GTPase regulator activity / RAF/MAP kinase cascade / small GTPase-mediated signal transduction / brush border / guanyl-nucleotide exchange factor activity / Ras protein signal transduction / nucleus / plasma membrane / cytosol
Similarity search - Function
Ral guanine nucleotide dissociation stimulator / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal ...Ral guanine nucleotide dissociation stimulator / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ral guanine nucleotide dissociation stimulator
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsHuang, L. / Weng, X.W. / Hofer, F. / Martin, G.S. / Kim, S.H.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Three-dimensional structure of the Ras-interacting domain of RalGDS.
Authors: Huang, L. / Weng, X. / Hofer, F. / Martin, G.S. / Kim, S.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary Crystallographic Analysis of the Ras Binding Domain of Ralgds, a Guanine Nucleotide Dissociation Stimulator of the Ral Protein
Authors: Huang, L. / Jancarik, J. / Kim, S.-H. / Hofer, F. / Martin, G.S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Activated Ras Interacts with the Ral Guanine Nucleotide Dissociation Stimulator
Authors: Hofer, F. / Fields, S. / Schneider, C. / Martin, G.S.
History
DepositionMar 5, 1997Processing site: BNL
Revision 1.0Mar 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RALGDSB
B: RALGDSB


Theoretical massNumber of molelcules
Total (without water)22,7022
Polymers22,7022
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.282, 30.714, 51.326
Angle α, β, γ (deg.)90.00, 94.57, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.219734, -0.826478, -0.518316), (-0.811699, -0.139838, 0.567089), (-0.541167, 0.545325, -0.640124)
Vector: 90.1868, 3.1041, 130.4588)

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Components

#1: Protein RALGDSB


Mass: 11350.771 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN WHICH BINDS TO ACTIVE RAS
Mutation: N-TERMINAL GS INHERITED FROM THE LINKER SEQUENCE OF THE CLONING VECTOR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RALGDS C-TERMINAL DOMAIN / Plasmid: PGEX98 FROM PGEX2T
Gene (production host): C-TERMINAL DOMAIN OF RALGDS FUSED TO GLUTATHIONINE S TRANSFERASE
Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: Q03386
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTERMINAL RESIDUE LYS 100 IN THE PDB FILE IS LYS 864 IN THE RAT RALGDS SEQUENCE.

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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: 1.8 Å3/Da / Density % sol: 30 %
Description: THIS STRUCTURE WAS SOLVED USING THE MAD DATA ON THE SELENOMETHIONINE MUTANT OF THE PROTEIN AT X4A NSLS. BUT THE STRUCTURE WAS REFINED AGAINST THE NATIVE DATA ABOVE.
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 8000, 0.1 M TRIS PH 8.5, AND 0.2 M CALCIUM ACETATE.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.5 mMdithiothreitol1drop
30.5 mMPMSF1drop
40.5 mMEDTA1drop
50.1 Mcalcium acetate1drop
60.05 mMTris-HCl1drop
710 %PEG80001drop
80.2 Mcalcium acetate1reservoir
90.1 MTris-HCl1reservoir
1020 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. obs: 6485 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.09 / Net I/σ(I): 16.7
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.92 / Rsym value: 0.251 / % possible all: 99.5
Reflection
*PLUS
Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MADSYSphasing
X-PLOR3.85model building
X-PLOR3.85refinement
X-PLOR3.85phasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→6 Å / Rfactor Rfree error: 0.04 / Data cutoff high absF: 15000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: H19A.PEP IS THE PEPTIDE BOND FIL
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -10 %RANDOM
Rwork0.212 ---
obs0.212 6209 84 %-
Displacement parametersBiso mean: 15 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 0 58 1453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: NO RESTRAINTS.
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 -10 %
Rwork0.261 408 -
obs--70.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1P19.PROX19.PRO
X-RAY DIFFRACTION2P11.WATH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.31

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