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- PDB-2ffq: The crystal structure of human neuronal Rab6B in its active GTPgS... -

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Basic information

Entry
Database: PDB / ID: 2ffq
TitleThe crystal structure of human neuronal Rab6B in its active GTPgS-bound form
ComponentsRas-related protein Rab-6B
KeywordsHYDROLASE / protein-nucleotide complex
Function / homology
Function and homology information


protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / 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 ...protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / 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 / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / endomembrane system / small monomeric GTPase / intracellular protein transport / neuron projection development / presynapse / cytoplasmic vesicle / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Ras-related protein Rab-6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGarcia-Saez, I. / Tcherniuk, S. / Kozielski, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: The structure of human neuronal Rab6B in the active and inactive form.
Authors: Garcia-Saez, I. / Tcherniuk, S. / Kozielski, F.
History
DepositionDec 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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_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-6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3573
Polymers19,7931
Non-polymers5642
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.885, 60.983, 63.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related protein Rab-6B / Rab6B


Mass: 19793.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6B / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NRW1, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.76 Å3/Da / Density % sol: 30.12 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 20% PEG3350, 0.2M ammonium nitrate , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.78→31.8 Å / Num. all: 13888 / Num. obs: 13846 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.052 / Rsym value: 0.048 / Net I/σ(I): 11.9
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1944 / Rsym value: 0.209 / % possible all: 97.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.202 1326 RANDOM
Rwork0.191 --
all0.193 13561 -
obs0.188 13155 -
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.78→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 33 132 1509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.259 217 -
Rwork0.217 --
obs-1838 90.3 %

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