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- PDB-1g16: CRYSTAL STRUCTURE OF SEC4-GDP -

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Basic information

Entry
Database: PDB / ID: 1g16
TitleCRYSTAL STRUCTURE OF SEC4-GDP
ComponentsRAS-RELATED PROTEIN SEC4
KeywordsSIGNALING PROTEIN / ENDOCYTOSIS/EXOCYTOSIS / G protein Rab / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


ascospore-type prospore assembly / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi vesicle fusion to target membrane / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / cellular bud neck / regulation of exocytosis ...ascospore-type prospore assembly / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi vesicle fusion to target membrane / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / cellular bud neck / regulation of exocytosis / trans-Golgi network transport vesicle / mating projection tip / endocytic recycling / vesicle docking involved in exocytosis / transport vesicle membrane / exocytosis / protein secretion / transport vesicle / Neutrophil degranulation / protein localization to plasma membrane / autophagy / vesicle / mitochondrial outer membrane / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / plasma membrane
Similarity search - Function
ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 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 ...ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 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
: / GUANOSINE-5'-DIPHOSPHATE / Ras-related protein SEC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
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.
History
DepositionOct 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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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
C: RAS-RELATED PROTEIN SEC4
D: RAS-RELATED PROTEIN SEC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46616
Polymers77,2224
Non-polymers2,24412
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.007, 56.379, 59.374
Angle α, β, γ (deg.)95.25, 101.68, 116.20
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

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


Mass: 19305.557 Da / Num. of mol.: 4 / Fragment: RESIDUES 18-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07560
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.7
Details: PEG 4000, 12% Cobalt Chloride, 70 mM Sodium cacodylate, pH 5.7, microbatch, temperature 21K
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl11
25 mM11MgCl2
312 %(v/v)PEG400011
470 mM11CoCl2
5100 mMsodium cacodylate11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.110.9797,0.9794,0.9796
SYNCHROTRONALS 5.0.120.9796,0.9794,0.9782
SYNCHROTRONALS 5.0.131.1000,0.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 22, 2000
ADSC QUANTUM 42CCDJan 22, 2000
ADSC QUANTUM 43CCDJan 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97941
30.97961
40.97821
51.11
60.97951
ReflectionResolution: 1.8→28.9 Å / Num. all: 117032 / Num. obs: 104861 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.89 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.258 / Num. unique all: 11775 / % possible all: 60.8
Reflection
*PLUS
Num. measured all: 408214
Reflection shell
*PLUS
% possible obs: 60.8 % / Mean I/σ(I) obs: 5.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.8→28.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1170816.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 9995 9.8 %RANDOM
Rwork0.276 ---
all0.276 115730 --
obs0.276 102210 88.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.58 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å23.67 Å24.82 Å2
2---2.98 Å22.69 Å2
3---0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5149 0 120 328 5597
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 645 9.5 %
Rwork0.349 6112 -
obs--58.1 %
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 DIFFRACTION4GDP.PARAMGDP.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_deg0.71

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