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- PDB-6s5f: Structure of the human RAB39B in complex with GMPPNP -

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Basic information

Entry
Database: PDB / ID: 6s5f
TitleStructure of the human RAB39B in complex with GMPPNP
ComponentsRas-related protein Rab-39B
KeywordsSTRUCTURAL GENOMICS / GTPase / Ras-related protein Rab-39B / GMPPNP / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Rab protein signal transduction / RAB geranylgeranylation / myosin V binding / RAB GEFs exchange GTP for GDP on RABs / vesicle-mediated transport / regulation of autophagy / synapse organization / cytoplasmic vesicle membrane / autophagy / protein transport ...Rab protein signal transduction / RAB geranylgeranylation / myosin V binding / RAB GEFs exchange GTP for GDP on RABs / vesicle-mediated transport / regulation of autophagy / synapse organization / cytoplasmic vesicle membrane / autophagy / protein transport / vesicle / neuron projection / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / plasma membrane
Similarity search - Function
Rab39 / small GTPase Rab1 family profile. / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GLYCINE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-39B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDiaz-Saez, L. / Jung, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative United Kingdom
CitationJournal: To Be Published
Title: Structure of the human RAB39B in complex with GMPPNP
Authors: Diaz-Saez, L. / Jung, S. / Huber, K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C.
History
DepositionJul 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-39B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6655
Polymers23,9811
Non-polymers6844
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-14 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.725, 35.285, 53.605
Angle α, β, γ (deg.)90.000, 107.510, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ras-related protein Rab-39B


Mass: 23981.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB39B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96DA2

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Non-polymers , 5 types, 111 molecules

#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.1 M HEPES pH 7.1, 19 % PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.7→50.28 Å / Num. obs: 20997 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/σ(I): 8.8 / Num. measured all: 134548 / Scaling rejects: 294
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7360.8421.811100.8430.3730.92399.9
9-50.286.50.05622.31600.9970.0230.0699.3
1.7-50.286.40.1058.8209970.9970.0450.11599.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A5J

2a5j


Resolution: 1.7→50.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.777 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.117
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 975 4.6 %RANDOM
Rwork0.1838 ---
obs0.186 20021 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.26 Å2 / Biso mean: 23.516 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20.98 Å2
2---0.16 Å20 Å2
3---0.8 Å2
Refinement stepCycle: final / Resolution: 1.7→50.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 41 107 1691
Biso mean--19.79 34.97 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131699
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171595
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6612318
X-RAY DIFFRACTIONr_angle_other_deg1.4341.5823685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8455212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62320.278108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40415305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9891520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 61 -
Rwork0.258 1480 -
all-1541 -
obs--99.81 %

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