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- PDB-1g17: CRYSTAL STRUCTURE OF SEC4-GUANOSINE-5'-(BETA,GAMMA)-IMIDOTRIPHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1g17
TitleCRYSTAL STRUCTURE OF SEC4-GUANOSINE-5'-(BETA,GAMMA)-IMIDOTRIPHOSPHATE
ComponentsRAS-RELATED PROTEIN SEC4
KeywordsSIGNALING PROTEIN / ENDOCYTOSIS/EXOCYTOSIS / G protein Rab / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homologyRAB geranylgeranylation / Neutrophil degranulation / Platelet degranulation / small GTPase Rab1 family profile. / Ras family / P-loop containing nucleoside triphosphate hydrolase / Small GTP-binding protein domain / Small GTPase / ascospore-type prospore assembly / membrane addition at site of cytokinesis ...RAB geranylgeranylation / Neutrophil degranulation / Platelet degranulation / small GTPase Rab1 family profile. / Ras family / P-loop containing nucleoside triphosphate hydrolase / Small GTP-binding protein domain / Small GTPase / ascospore-type prospore assembly / membrane addition at site of cytokinesis / incipient cellular bud site / vesicle fusion / vesicle docking involved in exocytosis / cellular bud neck / regulation of exocytosis / mating projection tip / Golgi to plasma membrane transport / Rab protein signal transduction / transport vesicle membrane / exocytosis / protein secretion / transport vesicle / protein localization to plasma membrane / intracellular protein transport / autophagy / mitochondrial outer membrane / vesicle / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / plasma membrane / Ras-related protein SEC4
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2 Å resolution
AuthorsStroupe, C. / Brunger, A.T.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of a Rab protein in its inactive and active conformations.
Authors: Stroupe, C. / Brunger, A.T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 10, 2000 / Release: Dec 11, 2000
RevisionDateData content typeGroupProviderType
1.0Dec 11, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN SEC4
B: RAS-RELATED PROTEIN SEC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4236
Polyers38,3302
Non-polymers1,0934
Water2,090116
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)84.504, 84.504, 86.469
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Cell settinghexagonal
Space group name H-MP 65

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Components

#1: Protein/peptide RAS-RELATED PROTEIN SEC4 / GTP-BINDING PROTEIN SEC4


Mass: 19164.871 Da / Num. of mol.: 2 / Fragment: RESIDUES 18-187
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Genus: Saccharomyces / Plasmid name: PGEX-4T-1 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P07560
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Formula: C10H17N6O13P3
Comment: GppNHp (GMPPNP, energy-carrying molecule analogue) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.32 / Density percent sol: 47.1 %
Crystal growTemp: 294 K / Method: vapor diffusion, hanging drop, with microseeding / pH: 7.7
Details: Polyethylene glycol 4000, 25% MgCl2, 200 mM Ethylene glycol, 30% Sodium HEPES, 100 mM, pH 7.7, vapor diffusion, hanging drop, with microseeding, temperature 294K
Crystal grow
*PLUS
Temp: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and reservoir solutions
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
125 mg/mlprotein1drop
220 mMTris-HCl1drop
35 mM1dropMgCl2
41 mMdithiothreitol1drop
5100 mM1dropNaCl
625 %(v/v)PEG40001reservoir
725-30 %(v/v)ethylene glycol1reservoir
80.2 M1reservoirMgCl2
9100 mMsodium HEPES1reservoir

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Data collection

Diffraction
IDMean temperatureCrystal ID
11001
21001
Source

Source: SYNCHROTRON

TypeSynchrotron siteBeamlineIdWavelengthWavelength
ALS BEAMLINE 5.0.1ALS5.0.110.9802,0.9800,0.9537
NSLS BEAMLINE X4ANSLSX4A21.2843
Detector
TypeIdDetectorCollection date
ADSC QUANTUM 41CCD1999-02-13
RIGAKU RAXIS IV2IMAGE PLATE1999-03-12
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.98021.0
20.98001.0
30.95371.0
41.28431.0
ReflectionB iso Wilson estimate: 15.9 Å2 / D resolution high: 2 Å / D resolution low: 38 Å / Number all: 23567 / Number obs: 23496 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.091 / NetI over sigmaI: 13.2 / Redundancy: 3.72 % / Percent possible obs: 99.7
Reflection shellRmerge I obs: 0.624 / Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Number unique all: 2322 / Redundancy: 3.48 % / Percent possible all: 99.4
Reflection
*PLUS
Number measured all: 87371
Reflection shell
*PLUS
Percent possible obs: 99.4 / MeanI over sigI obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefineR Free selection details: RANDOM / Data cutoff high absF: 3712802.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 38 / Solvent model param ksol: 0.342
Displacement parametersB iso mean: 34.1 Å2 / Aniso B11: -3.76 Å2 / Aniso B12: 0.87 Å2 / Aniso B13: 0 Å2 / Aniso B22: -3.76 Å2 / Aniso B23: 0 Å2 / Aniso B33: 7.52 Å2
Least-squares processR factor R free: 0.292 / R factor R free error: 0.004 / R factor R work: 0.264 / R factor all: 0.264 / R factor obs: 0.264 / Highest resolution: 2 Å / Lowest resolution: 33.7 Å / Number reflection R free: 4205 / Number reflection all: 46649 / Number reflection obs: 43560 / Percent reflection R free: 9.7 / Percent reflection obs: 93.8
Refine analyzeLuzzati coordinate error free: 0.37 Å / Luzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.36 Å / Luzzati sigma a obs: 0.35 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 33.7 Å
Number of atoms included #LASTProtein: 2662 / Nucleic acid: 0 / Ligand: 66 / Solvent: 116 / Total: 2844
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.351.50
X-RAY DIFFRACTIONc_mcangle_it2.232.00
X-RAY DIFFRACTIONc_scbond_it1.772.00
X-RAY DIFFRACTIONc_scangle_it2.652.50
Refine LS shellHighest resolution: 2 Å / R factor R free: 0.38 / R factor R free error: 0.023 / R factor R work: 0.375 / Lowest resolution: 2.07 Å / Number reflection R free: 265 / Number reflection R work: 3056 / Total number of bins used: 10 / Percent reflection R free: 8 / Percent reflection obs: 71.5
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GMPPNP.PARAMGMPPNP.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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