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- PDB-4dkx: Crystal Structure of the Rab 6A'(Q72L) -

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Basic information

Entry
Database: PDB / ID: 4dkx
TitleCrystal Structure of the Rab 6A'(Q72L)
ComponentsRas-related protein Rab-6A
KeywordsPROTEIN TRANSPORT / GTP binding fold / Membrane trafficking / GTP / Cytosol
Function / homology
Function and homology information


peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / intra-Golgi vesicle-mediated transport ...peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / intra-Golgi vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs / antigen processing and presentation / endomembrane system / localization / secretory granule membrane / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / neuron projection development / cytoplasmic vesicle / protein domain specific binding / Golgi membrane / GTPase activity / Neutrophil degranulation / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / extracellular exosome / membrane / plasma membrane / 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 / P-loop containing nucleoside triphosphate hydrolase ...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-6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, H.H. / Shin, Y.-C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of Rab6A'(Q72L) mutant reveals unexpected GDP/Mg2+ binding with opened GTP-binding domain
Authors: Shin, Y.-C. / Yoon, J.H. / Jang, T.-H. / Kim, S.Y. / Heo, W.D. / So, I. / Jeon, J.-H. / Park, H.H.
History
DepositionFeb 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_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

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Assembly

Deposited unit
A: Ras-related protein Rab-6A
B: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2016
Polymers49,2662
Non-polymers9354
Water4,450247
1
A: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1003
Polymers24,6331
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1003
Polymers24,6331
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.838, 96.780, 109.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

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Components

#1: Protein Ras-related protein Rab-6A / RAB GTPase / Rab-6


Mass: 24632.896 Da / Num. of mol.: 2 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6A, RAB6 / Production host: Escherichia coli (E. coli) / References: UniProt: P20340
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 62-88 ARE BASED ON ISOFORM 2 OF RAB6A_HUMAN (P20340). RESIDUES 62, 87 AND 88 ARE ILE, ALA ...RESIDUES 62-88 ARE BASED ON ISOFORM 2 OF RAB6A_HUMAN (P20340). RESIDUES 62, 87 AND 88 ARE ILE, ALA AND ALA RESPECTIVELY IN ISOFORM 2.

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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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 200mM Calcium acetate, 100mM Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.999 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 9, 2010
RadiationMonochromator: GRAPHITE / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.9→48.39 Å / Num. obs: 31899 / % possible obs: 70 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.9 Å / % possible all: 70

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.39 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.093 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25036 1613 5.1 %RANDOM
Rwork0.19644 ---
obs0.19913 30283 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 58 247 2789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222587
X-RAY DIFFRACTIONr_angle_refined_deg3.1751.9893495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16623.109119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3841525
X-RAY DIFFRACTIONr_chiral_restr0.1880.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021867
X-RAY DIFFRACTIONr_mcbond_it1.3991.51520
X-RAY DIFFRACTIONr_mcangle_it2.38122458
X-RAY DIFFRACTIONr_scbond_it4.06131067
X-RAY DIFFRACTIONr_scangle_it6.2344.51037
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 118 -
Rwork0.229 2198 -
obs--99.78 %

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