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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 / 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 / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / 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 / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / regulation of exocytosis / mating projection tip / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein SEC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_conn.ptnr2_label_seq_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

Downloads & links

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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
Polymers38,3302
Non-polymers1,0934
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP65

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Components

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


Mass: 19164.871 Da / Num. of mol.: 2 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 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
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common 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 temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONALS 5.0.110.9802,0.9800,0.9537
SYNCHROTRONNSLS X4A21.2843
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 13, 1999
RIGAKU RAXIS IV2IMAGE PLATEMar 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98021
20.981
30.95371
41.28431
ReflectionResolution: 2→38 Å / Num. all: 23567 / Num. obs: 23496 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.72 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.624 / Num. unique all: 2322 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 87371
Reflection shell
*PLUS
% possible obs: 99.4 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2→33.7 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3712802.4 / 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
Rfree0.292 4205 9.7 %RANDOM
Rwork0.264 ---
all0.264 46649 --
obs0.264 43560 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.76 Å20.87 Å20 Å2
2---3.76 Å20 Å2
3---7.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 66 116 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_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 265 8 %
Rwork0.375 3056 -
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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