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- PDB-1yzl: GppNHp-Bound Rab9 GTPase -

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Basic information

Entry
Database: PDB / ID: 1yzl
TitleGppNHp-Bound Rab9 GTPase
ComponentsRas-related protein Rab-9A
KeywordsPROTEIN TRANSPORT / Rab GTPase / Rab9 / vesicular trafficking
Function / homology
Function and homology information


RHOBTB3 ATPase cycle / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Rab protein signal transduction / phagocytic vesicle / cytoplasmic vesicle membrane / small monomeric GTPase / phagocytic vesicle membrane / GDP binding ...RHOBTB3 ATPase cycle / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Rab protein signal transduction / phagocytic vesicle / cytoplasmic vesicle membrane / small monomeric GTPase / phagocytic vesicle membrane / GDP binding / late endosome / melanosome / protein transport / lysosome / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / identical protein binding / plasma membrane
Similarity search - Function
Rab9 / 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 ...Rab9 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-9A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsEathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
CitationJournal: Nature / Year: 2005
Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5.
Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7683
Polymers20,2221
Non-polymers5472
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.325, 68.325, 83.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ras-related protein Rab-9A / Rab-9 / Sid 99


Mass: 20221.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab9a, Rab9, Sid99 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: Q9R0M6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.86 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 6000, 200mM Magnesium Chloride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 21, 2003 / Details: osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 19409 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 26.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5 / Num. unique all: 19418 / Rsym value: 0.394

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyalanine Rab4 GTPase

Resolution: 1.85→4.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.596 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22084 925 5.1 %RANDOM
Rwork0.19179 ---
all0.215 19418 --
obs0.19327 17308 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.85→4.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 33 253 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221433
X-RAY DIFFRACTIONr_bond_other_d0.0010.021233
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9591944
X-RAY DIFFRACTIONr_angle_other_deg0.8132868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62224.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79715234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.894158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
X-RAY DIFFRACTIONr_nbd_refined0.2140.2285
X-RAY DIFFRACTIONr_nbd_other0.1850.21212
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2713
X-RAY DIFFRACTIONr_nbtor_other0.0790.2742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1190.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8841.51108
X-RAY DIFFRACTIONr_mcbond_other0.1031.5353
X-RAY DIFFRACTIONr_mcangle_it0.95821367
X-RAY DIFFRACTIONr_scbond_it1.3443715
X-RAY DIFFRACTIONr_scangle_it1.9144.5577
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.854→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 51 -
Rwork0.21 1131 -
obs--98.17 %

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