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- PDB-6s5h: Structure of the human RAB38 in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 6s5h
TitleStructure of the human RAB38 in complex with GTP
ComponentsRas-related protein Rab-38
KeywordsSTRUCTURAL GENOMICS / GTPase / Ras-related protein Rab-38 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


BLOC-2 complex binding / AP-3 adaptor complex binding / phagosome acidification / positive regulation of phosphatidylcholine biosynthetic process / AP-1 adaptor complex binding / endosome to melanosome transport / platelet dense granule organization / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / positive regulation of melanin biosynthetic process ...BLOC-2 complex binding / AP-3 adaptor complex binding / phagosome acidification / positive regulation of phosphatidylcholine biosynthetic process / AP-1 adaptor complex binding / endosome to melanosome transport / platelet dense granule organization / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / positive regulation of melanin biosynthetic process / GTP-dependent protein binding / melanosome membrane / RAB geranylgeranylation / melanosome organization / RAB GEFs exchange GTP for GDP on RABs / protein localization to membrane / positive regulation of protein localization to cell periphery / small GTPase-mediated signal transduction / vesicle-mediated transport / phagocytic vesicle / mitochondrion organization / intracellular protein transport / trans-Golgi network / phagocytic vesicle membrane / melanosome / protein transport / cell body / lysosome / early endosome / GTPase activity / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rab29/Rab38/Rab32 / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BROMIDE ION / GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 RAB38 in complex with GTP
Authors: Diaz-Saez, L. / a 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,78915
Polymers23,4431
Non-polymers1,34614
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint0 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.804, 144.174, 77.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-308-

EDO

21A-313-

BR

31A-505-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ras-related protein Rab-38 / Melanoma antigen NY-MEL-1


Mass: 23442.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues not visible in the structure: 135 to 141 and 185 to end
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB38 / Production host: Escherichia coli (E. coli) / References: UniProt: P57729

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 % PEG3350, 10 % ethylene glycol, 0.1 M Bis-Tris-propane pH6 .5, 0.2 M sodium bromide

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2→38.76 Å / Num. obs: 14044 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.037 / Rrim(I) all: 0.135 / Net I/σ(I): 12.2 / Num. measured all: 183431 / Scaling rejects: 206
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allMean I/σ(I) obs
2-2.0513.10.64910050.9510.1850.675100
8.94-38.7611.20.0771910.9990.0230.08199.3
2-38.7613.10.13140440.9980.0370.13510012.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OEC

5oec


Resolution: 2→38.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.014 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 697 5 %RANDOM
Rwork0.1633 ---
obs0.1656 13318 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.48 Å2 / Biso mean: 28.47 Å2 / Biso min: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0 Å2-0 Å2
2--2.96 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: final / Resolution: 2→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 72 145 1615
Biso mean--36.17 39.32 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131554
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171454
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6492105
X-RAY DIFFRACTIONr_angle_other_deg1.3151.5813380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7595195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59822.59381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32115270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.225159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02327
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 43 -
Rwork0.19 958 -
all-1001 -
obs--99.8 %

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