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- PDB-2if0: Crystal Structure of mouse Rab27b bound to GDP in monoclinic spac... -

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Basic information

Entry
Database: PDB / ID: 2if0
TitleCrystal Structure of mouse Rab27b bound to GDP in monoclinic space group
ComponentsRas-related protein Rab-27B
KeywordsSIGNALING PROTEIN / Rab27 / GTPase / Rab / GDP / swapping
Function / homology
Function and homology information


RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / zymogen granule membrane / anterograde axonal protein transport / Platelet degranulation / exocytic vesicle / Golgi stack / multivesicular body sorting pathway / myosin V binding / trans-Golgi network transport vesicle ...RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / zymogen granule membrane / anterograde axonal protein transport / Platelet degranulation / exocytic vesicle / Golgi stack / multivesicular body sorting pathway / myosin V binding / trans-Golgi network transport vesicle / regulation of exocytosis / multivesicular body membrane / exocytosis / positive regulation of exocytosis / synaptic vesicle endocytosis / axon cytoplasm / small monomeric GTPase / G protein activity / secretory granule / synaptic vesicle membrane / GDP binding / melanosome / late endosome / apical plasma membrane / protein domain specific binding / GTPase activity / GTP binding / Golgi apparatus
Similarity search - Function
Rab27a/b / 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 ...Rab27a/b / 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 Rab-27B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChavas, L.M.G. / Torii, S. / Kamikubo, H. / Kawasaki, M. / Ihara, K. / Kato, R. / Kataoka, M. / Izumi, T. / Wakatsuki, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the small GTPase Rab27b shows an unexpected swapped dimer
Authors: Chavas, L.M.G. / Torii, S. / Kamikubo, H. / Kawasaki, M. / Ihara, K. / Kato, R. / Kataoka, M. / Izumi, T. / Wakatsuki, S.
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_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 Rab-27B
B: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3866
Polymers45,4512
Non-polymers9354
Water25214
1
A: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1933
Polymers22,7261
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1933
Polymers22,7261
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-69 kcal/mol
Surface area19180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.960, 64.755, 153.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chain A and chain B

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Components

#1: Protein Ras-related protein Rab-27B


Mass: 22725.701 Da / Num. of mol.: 2 / Fragment: soluble domain / Mutation: Q78L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LysS / References: UniProt: Q99P58, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: MPD, Cacodylate, pH 5.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: May 31, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→76.69 Å / Num. obs: 14358 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.109 / Χ2: 0.96
Reflection shellResolution: 2.8→2.9 Å / % possible obs: 97.4 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.418 / Num. measured obs: 1367 / Num. unique all: 1367 / Χ2: 1.022 / % possible all: 97.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å40.12 Å
Translation4 Å40.12 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IEZ

2iez


Resolution: 2.8→40.1 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.843 / SU B: 15.586 / SU ML: 0.303 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.967 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31492 704 5 %RANDOM
Rwork0.25903 ---
all0.263 ---
obs0.26163 13384 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.486 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--4.24 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 58 14 2921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.9824012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4925345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24223.96149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67115522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0351522
X-RAY DIFFRACTIONr_chiral_restr0.070.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022218
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21239
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21984
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4691.51777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82622786
X-RAY DIFFRACTIONr_scbond_it0.89731370
X-RAY DIFFRACTIONr_scangle_it1.5454.51226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 57 -
Rwork0.321 961 -
all-1018 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2309-0.8603-0.58323.49881.57692.68020.07080.0240.12430.1867-0.0231-0.3382-0.12380.1788-0.0476-0.26350.0226-0.0486-0.03890.0379-0.131820.25730.2269-20.0007
22.39950.98751.49420.91891.91094.2076-0.11350.21380.03290.44210.1643-0.1320.23160.511-0.0508-0.08140.0587-0.0018-0.270.0338-0.127-4.3665-3.3262-18.0739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 3013 - 32
2X-RAY DIFFRACTION1AA94 - 18596 - 187
3X-RAY DIFFRACTION2BB11 - 3013 - 32
4X-RAY DIFFRACTION2BB94 - 18596 - 187

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