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- PDB-2f9m: 3D structure of active human Rab11b GTPase -

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Basic information

Entry
Database: PDB / ID: 2f9m
Title3D structure of active human Rab11b GTPase
ComponentsRAB11B, member RAS oncogene family
KeywordsHYDROLASE / Rab11b GTPase / vesicle transport
Function / homology
Function and homology information


constitutive secretory pathway / regulation of endocytic recycling / transferrin transport / regulated exocytosis / melanosome transport / receptor recycling / amyloid-beta clearance by transcytosis / regulation of protein localization to cell surface / myosin V binding / RAB geranylgeranylation ...constitutive secretory pathway / regulation of endocytic recycling / transferrin transport / regulated exocytosis / melanosome transport / receptor recycling / amyloid-beta clearance by transcytosis / regulation of protein localization to cell surface / myosin V binding / RAB geranylgeranylation / cellular response to acidic pH / endocytic recycling / establishment of protein localization to membrane / TBC/RABGAPs / insulin secretion involved in cellular response to glucose stimulus / phagocytic vesicle / regulation of monoatomic anion transport / small monomeric GTPase / recycling endosome / G protein activity / synaptic vesicle membrane / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / synaptic vesicle / cadherin binding / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome / cytosol
Similarity search - Function
: / 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 ...: / 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 / NICKEL (II) ION / Ras-related protein Rab-11B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsScapin, S.M.N. / Guimaraes, B.G. / Zanchin, N.I.T.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: The crystal structure of the small GTPase Rab11b reveals critical differences relative to the Rab11a isoform.
Authors: Scapin, S.M. / Carneiro, F.R. / Alves, A.C. / Medrano, F.J. / Guimaraes, B.G. / Zanchin, N.I.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: RAB11B, member RAS oncogene family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1375
Polymers22,4731
Non-polymers6644
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.611, 85.409, 86.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1205-

HOH

21A-1244-

HOH

31A-1320-

HOH

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Components

#1: Protein RAB11B, member RAS oncogene family


Mass: 22473.238 Da / Num. of mol.: 1 / Fragment: GTPase domain, residues 8 to 205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCYTEXP3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q15907, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: reservoir solution: 0.1M Tris-HCl pH8.5, 1M lithium sulfate, 0.01M nickel chloride. Protein sample: 68 mg/ml Rab11b-GppNHp, 10mM Tris-HCl pH7.4, 0.1mM magnesium chloride., VAPOR DIFFUSION, ...Details: reservoir solution: 0.1M Tris-HCl pH8.5, 1M lithium sulfate, 0.01M nickel chloride. Protein sample: 68 mg/ml Rab11b-GppNHp, 10mM Tris-HCl pH7.4, 0.1mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 11, 2004
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 1.95→33.48 Å / Num. obs: 18222 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rsym value: 0.09 / Net I/σ(I): 19.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 9 % / Mean I/σ(I) obs: 6.6 / Rsym value: 0.331 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.655 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20529 940 5.1 %RANDOM
Rwork0.16263 ---
all0.16479 18438 --
obs0.16479 17437 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 35 286 1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221513
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.972051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32423.64974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48315265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8871513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021122
X-RAY DIFFRACTIONr_nbd_refined0.2120.2921
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2287
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.240
X-RAY DIFFRACTIONr_mcbond_it0.561.5915
X-RAY DIFFRACTIONr_mcangle_it1.03621449
X-RAY DIFFRACTIONr_scbond_it1.7633671
X-RAY DIFFRACTIONr_scangle_it2.9264.5602
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 64 -
Rwork0.204 1263 -
obs--100 %

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