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

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Basic information

Entry
Database: PDB / ID: 2iez
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: 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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
H: Ras-related protein Rab-27B
I: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,80512
Polymers98,8724
Non-polymers1,9338
Water68538
1
A: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2013
Polymers24,7181
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2013
Polymers24,7181
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2013
Polymers24,7181
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2013
Polymers24,7181
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Ras-related protein Rab-27B
B: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4026
Polymers49,4362
Non-polymers9674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-72 kcal/mol
Surface area19960 Å2
MethodPISA, PQS
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H: Ras-related protein Rab-27B
I: Ras-related protein Rab-27B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4026
Polymers49,4362
Non-polymers9674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-72 kcal/mol
Surface area19630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)170.496, 63.348, 80.845
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a monomer. There are 4 biological units in the asymmetric unit (chain A and chain B and chain H and chain I)

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Components

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


Mass: 24717.943 Da / Num. of mol.: 4 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: MPD, CaCl2, Hepes, pH 7.0, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→84.21 Å / Num. obs: 20069 / % possible obs: 86.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.121 / Χ2: 1.019
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.484 / Num. unique all: 1770 / % possible all: 76.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å35.64 Å
Translation4 Å35.64 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IEY

2iey


Resolution: 2.8→35.6 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.815 / SU B: 23.271 / SU ML: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36315 952 5.1 %RANDOM
Rwork0.2623 ---
obs0.26743 17648 87.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.422 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å2-0.06 Å2
2--2.59 Å20 Å2
3----5.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 116 38 5754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9837878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3424.124291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.044151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.571542
X-RAY DIFFRACTIONr_chiral_restr0.0750.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22520
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23825
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4781.53525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84925496
X-RAY DIFFRACTIONr_scbond_it0.88432663
X-RAY DIFFRACTIONr_scangle_it1.4754.52382
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
Rfree0.417 64 -
Rwork0.288 1249 -
all-1313 -
obs--83.52 %
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)
10.3693-0.35830.68740.3476-0.6671.2796-0.02470.40050.434-0.2602-0.16110.3552-0.047-0.30210.18580.1505-0.14180.07890.0802-0.1392-0.0778-23.8908-52.817124.3624
22.88632.011.06171.91373.180211.9843-0.2927-0.20030.3072-0.0830.04410.19510.35950.07140.2485-0.05730.07930.0241-0.7060.1386-0.237-50.0889-21.29320.433
30.9045-1.0308-2.67491.37762.223311.2704-0.6174-0.58691.16440.15260.5566-0.16550.7493-0.65220.0607-0.3026-0.02790.07470.3819-0.2574-0.0304-9.4014-12.745221.9492
42.54761.7848-1.72456.2375-2.40516.35330.11790.17270.25140.3205-0.1564-0.168-0.15590.01420.0385-0.283-0.035-0.0615-0.2947-0.0697-0.4519-30.2086-27.8179-10.3406
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
5X-RAY DIFFRACTION3HC11 - 3013 - 32
6X-RAY DIFFRACTION3HC94 - 18596 - 187
7X-RAY DIFFRACTION4ID11 - 3013 - 32
8X-RAY DIFFRACTION4ID94 - 18596 - 187

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