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- PDB-2iey: Crystal Structure of mouse Rab27b bound to GDP in hexagonal space... -

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Basic information

Entry
Database: PDB / ID: 2iey
TitleCrystal Structure of mouse Rab27b bound to GDP in hexagonal 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 / multivesicular body sorting pathway / myosin V binding / trans-Golgi network transport vesicle / multivesicular body membrane / Golgi stack ...RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / zymogen granule membrane / anterograde axonal protein transport / Platelet degranulation / multivesicular body sorting pathway / myosin V binding / trans-Golgi network transport vesicle / multivesicular body membrane / Golgi stack / positive regulation of exocytosis / synaptic vesicle endocytosis / axon cytoplasm / small monomeric GTPase / GDP binding / synaptic vesicle membrane / melanosome / late endosome / G protein activity / apical plasma membrane / protein domain specific binding / GTPase activity / GTP binding / Golgi apparatus
Similarity search - Function
Rab27a/b / : / Small GTPase Rab domain 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 ...Rab27a/b / : / Small GTPase Rab domain 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
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-27B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.18 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: Version format compliance
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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)45,8774
Polymers44,9912
Non-polymers8862
Water19811
1
A: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9392
Polymers22,4961
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9392
Polymers22,4961
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Ras-related protein Rab-27B
B: Ras-related protein Rab-27B
hetero molecules

A: Ras-related protein Rab-27B
B: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7558
Polymers89,9824
Non-polymers1,7734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area18260 Å2
ΔGint-123 kcal/mol
Surface area33440 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-53 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.061, 66.061, 379.988
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
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: 22495.502 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): DL41 / References: UniProt: Q99P58, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: PEG 10000, Hepes, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9789 Å
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Nov 22, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.18→63.37 Å / Num. obs: 9142 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.8 % / Rmerge(I) obs: 0.111 / Χ2: 2.03
Reflection shellResolution: 3.18→3.31 Å / % possible obs: 100 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.693 / Num. measured obs: 1554 / Num. unique all: 1554 / Χ2: 1.645 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.040.2490.030.517
2Se600.4320.2050.0350.738
3Se600.8290.5010.0810.432
4Se600.8340.5960.0710.456
5Se600.450.0160.0530.481
6Se600.8160.6380.0750.463
7Se600.3020.6180.0280.366
8Se10.0030.3630.0010.054
9Se600.1370.5790.0220.248
Phasing dmFOM : 0.69 / FOM acentric: 0.71 / FOM centric: 0.66 / Reflection: 8389 / Reflection acentric: 6062 / Reflection centric: 2327
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.1-36.5440.920.960.9458177281
5.7-9.10.840.890.761251770481
4.6-5.70.830.870.7314651023442
4-4.60.780.820.6614451079366
3.4-40.620.640.5423861884502
3.2-3.40.380.40.3313841129255

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVE2.05phasing
RESOLVE2.05phasing
REFMAC5.2.0019refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.18→36.5 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.842 / SU B: 34.386 / SU ML: 0.562 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.632 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3455 430 4.8 %RANDOM
Rwork0.28878 ---
obs0.29152 8610 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.356 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å21.42 Å20 Å2
2--2.84 Å20 Å2
3----4.26 Å2
Refinement stepCycle: LAST / Resolution: 3.18→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 56 11 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222781
X-RAY DIFFRACTIONr_bond_other_d0.0010.021890
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9843762
X-RAY DIFFRACTIONr_angle_other_deg0.86134572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86423.957139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26715486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3381520
X-RAY DIFFRACTIONr_chiral_restr0.070.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
X-RAY DIFFRACTIONr_nbd_refined0.2210.2678
X-RAY DIFFRACTIONr_nbd_other0.1980.22065
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21329
X-RAY DIFFRACTIONr_nbtor_other0.0870.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5411.51958
X-RAY DIFFRACTIONr_mcbond_other0.0631.5662
X-RAY DIFFRACTIONr_mcangle_it0.66622607
X-RAY DIFFRACTIONr_scbond_it0.78631366
X-RAY DIFFRACTIONr_scangle_it1.1074.51155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.183→3.265 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.539 32 -
Rwork0.374 570 -
all-570 -
obs--95.56 %
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)
10.9191-0.25053.24357.93770.786111.8010.12940.13450.2867-0.38080.152-1.0358-0.49190.0282-0.2814-0.7709-0.10810.2213-0.1671-0.4579-0.485421.7267-6.5438-15.9995
22.02170.38652.96774.07794.90069.0459-0.5943-0.7465-0.90180.9104-0.10030.89160.5957-2.32910.6946-0.35-0.09310.05770.9016-0.4526-0.119861.8546-15.2773-6.4588
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 - 18496 - 186

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