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- PDB-5di3: Crystal structure of Arl13B in complex with Arl3 of Chlamydomonas... -

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Basic information

Entry
Database: PDB / ID: 5di3
TitleCrystal structure of Arl13B in complex with Arl3 of Chlamydomonas reinhardtii
Components
  • ADP-ribosylation factor-like protein 13B
  • ADP-ribosylation factor-like protein 3
KeywordsHYDROLASE / G-protein / ADP ribosylation like protein / Complex / Guanine nucleotide exchange factor
Function / homology
Function and homology information


ciliary membrane / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor-like protein 13B / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGotthardt, K. / Lokaj, M. / Falk, N. / Koerner, C. / Giessl, A. / Wittinghofer, A.
CitationJournal: Elife / Year: 2015
Title: A G-protein activation cascade from Arl13B to Arl3 and implications for ciliary targeting of lipidated proteins.
Authors: Gotthardt, K. / Lokaj, M. / Koerner, C. / Falk, N. / Giel, A. / Wittinghofer, A.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ADP-ribosylation factor-like protein 13B
A: ADP-ribosylation factor-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2386
Polymers50,1452
Non-polymers1,0934
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-28 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.100, 68.800, 120.000
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 13B / CrArl13B


Mass: 29268.100 Da / Num. of mol.: 1 / Fragment: UNP residues 18-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ARL13, CHLREDRAFT_195529 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: A8INQ0
#2: Protein ADP-ribosylation factor-like protein 3


Mass: 20876.908 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
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris pH 8.5, 25 % PEG 6000 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16944 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 60.077 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.071 / Χ2: 0.98 / Net I/σ(I): 17.56 / Num. measured all: 109004
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.60.9020.6283.2612447184118400.6899.9
2.6-2.70.9470.4414.4510396157115700.47999.9
2.7-2.850.9670.3155.8212728199519950.343100
2.85-30.9880.2089.0210940161816170.22699.9
3-3.250.9950.13412.5313676205720560.146100
3.25-3.50.9960.08518.679537152215220.093100
3.5-40.9980.05925.4613278204120390.06499.9
4-50.9990.04233.0812720206620660.046100
5-500.9990.03437.4613282225422390.03899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BH6

3bh6


Resolution: 2.5→29.843 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 848 5.01 %
Rwork0.199 --
obs0.2009 16929 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.06 Å2 / Biso mean: 65.9867 Å2 / Biso min: 33.73 Å2
Refinement stepCycle: final / Resolution: 2.5→29.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 66 29 2995
Biso mean--54.32 55.03 -
Num. residues----368

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