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- PDB-5de3: The Crystal structure of Chlamydomonas reinhardtii Arl3 bound to ... -

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Basic information

Entry
Database: PDB / ID: 5de3
TitleThe Crystal structure of Chlamydomonas reinhardtii Arl3 bound to GppNHp
ComponentsADP-ribosylation factor-like protein 3
KeywordsHYDROLASE / G-protein / ADP ribosylation factor like
Function / homology
Function and homology information


spindle / protein transport / cell cycle / cell division / Golgi membrane / GTPase activity / GTP binding / nucleus
Similarity search - Function
ADP-ribosylation factor-like protein 2/3 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...ADP-ribosylation factor-like protein 2/3 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.417 Å
AuthorsGotthardt, K. / Lokaj, M. / Wittinghofer, A.
CitationJournal: To Be Published
Title: The Crystal structure of Chlamydomonas reinhardtii Arl3 bound to GppNHp
Authors: Gotthardt, K. / Lokaj, M. / Wittinghofer, A.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: ADP-ribosylation factor-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6653
Polymers19,1191
Non-polymers5472
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-13 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.840, 43.330, 80.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-ribosylation factor-like protein 3


Mass: 19118.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ARL3, CHLREDRAFT_128761 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: A8ISN6
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Lithium Acetate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 51299 / % possible obs: 91.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.79
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.26 / % possible all: 68.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bh6

3bh6


Resolution: 1.417→29.558 Å / FOM work R set: 0.8292 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 2552 4.97 %
Rwork0.2072 48747 -
obs0.2083 51299 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.45 Å2 / Biso mean: 28.82 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: final / Resolution: 1.417→29.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 33 61 1402
Biso mean--26.14 31.61 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011363
X-RAY DIFFRACTIONf_angle_d1.1351849
X-RAY DIFFRACTIONf_chiral_restr0.047210
X-RAY DIFFRACTIONf_plane_restr0.005229
X-RAY DIFFRACTIONf_dihedral_angle_d15.286508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4172-1.44440.29261040.3141963206768
1.4444-1.47390.30831370.29122586272392
1.4739-1.50590.27391430.26962697284094
1.5059-1.5410.26211440.25262700284495
1.541-1.57950.21031390.2472714285396
1.5795-1.62220.27721420.23462782292497
1.6222-1.66990.28131470.23132736288396
1.6699-1.72380.25381420.24032765290797
1.7238-1.78540.24951460.23172701284796
1.7854-1.85690.25131400.2292766290697
1.8569-1.94140.271470.22912820296798
1.9414-2.04380.22681440.21862771291598
2.0438-2.17180.27041490.21572792294198
2.1718-2.33940.31581450.20542802294798
2.3394-2.57470.20771420.20822730287296
2.5747-2.9470.22621490.21822823297299
2.947-3.71170.21771440.1922828297299
3.7117-29.56490.18571480.17672771291997

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