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- PDB-4v0n: Crystal structure of BBS1N in complex with ARL6DN, soaked with mercury -

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Basic information

Entry
Database: PDB / ID: 4v0n
TitleCrystal structure of BBS1N in complex with ARL6DN, soaked with mercury
Components
  • ARF-LIKE SMALL GTPASE
  • BARDET-BIEDL SYNDROME 1 PROTEINBardet–Biedl syndrome
KeywordsHYDROLASE/STRUCTURAL PROTEIN / HYDROLASE-STRUCTURAL PROTEIN COMPLEX / BBSOME / GTP / COAT COMPLEX
Function / homology
Function and homology information


BBSome / protein localization to cilium / non-motile cilium assembly / axoneme / cilium assembly / vesicle-mediated transport / intracellular protein transport / GTPase activity / GTP binding
Similarity search - Function
Bardet-Biedl syndrome 1 protein / Bardet-Biedl syndrome 1, N-terminal / Ciliary BBSome complex subunit 1 / 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 / Quinoprotein alcohol dehydrogenase-like superfamily / Small GTP-binding protein domain ...Bardet-Biedl syndrome 1 protein / Bardet-Biedl syndrome 1, N-terminal / Ciliary BBSome complex subunit 1 / 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 / Quinoprotein alcohol dehydrogenase-like superfamily / 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
GUANOSINE-5'-TRIPHOSPHATE / : / Bardet-biedl syndrome 1 protein / Uncharacterized protein
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.131 Å
AuthorsMourao, A. / Lorentzen, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural Basis for Membrane Targeting of the Bbsome by Arl6
Authors: Mourao, A. / Nager, A.R. / Nachury, M.V. / Lorentzen, E.
History
DepositionSep 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARF-LIKE SMALL GTPASE
B: BARDET-BIEDL SYNDROME 1 PROTEIN
C: ARF-LIKE SMALL GTPASE
D: BARDET-BIEDL SYNDROME 1 PROTEIN
E: ARF-LIKE SMALL GTPASE
F: BARDET-BIEDL SYNDROME 1 PROTEIN
G: ARF-LIKE SMALL GTPASE
H: BARDET-BIEDL SYNDROME 1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,32273
Polymers260,6998
Non-polymers13,62465
Water0
1
C: ARF-LIKE SMALL GTPASE
D: BARDET-BIEDL SYNDROME 1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33017
Polymers65,1752
Non-polymers3,15515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-133.9 kcal/mol
Surface area19940 Å2
MethodPISA
2
G: ARF-LIKE SMALL GTPASE
H: BARDET-BIEDL SYNDROME 1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,73119
Polymers65,1752
Non-polymers3,55617
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-132.1 kcal/mol
Surface area21010 Å2
MethodPISA
3
A: ARF-LIKE SMALL GTPASE
B: BARDET-BIEDL SYNDROME 1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,53018
Polymers65,1752
Non-polymers3,35616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-132.1 kcal/mol
Surface area21520 Å2
MethodPISA
4
E: ARF-LIKE SMALL GTPASE
F: BARDET-BIEDL SYNDROME 1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,73119
Polymers65,1752
Non-polymers3,55617
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-194.1 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.745, 123.745, 443.709
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
ARF-LIKE SMALL GTPASE / ARL6


Mass: 18806.646 Da / Num. of mol.: 4 / Fragment: GTPASE, RESIDUES 16-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8JF99
#2: Protein
BARDET-BIEDL SYNDROME 1 PROTEIN / Bardet–Biedl syndrome / BBS1


Mass: 46368.062 Da / Num. of mol.: 4 / Fragment: WD40, RESIDUES 1-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8JEA1
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: Hg

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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: 3.77 Å3/Da / Density % sol: 67.39 % / Description: NONE
Crystal growDetails: 29% PEG400, 0.1M TRIS PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0075
DetectorType: DECTRIS PILATUS 2MF / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0075 Å / Relative weight: 1
ReflectionResolution: 3.13→50 Å / Num. obs: 70112 / % possible obs: 99.2 % / Observed criterion σ(I): 1.7 / Redundancy: 13.2 % / Biso Wilson estimate: 104 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.6
Reflection shellResolution: 3.13→3.24 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.7 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.131→96.498 Å / SU ML: 0.42 / σ(F): 1.88 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 6643 5 %
Rwork0.2126 --
obs0.2145 70096 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.131→96.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14343 0 189 0 14532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114775
X-RAY DIFFRACTIONf_angle_d1.47620201
X-RAY DIFFRACTIONf_dihedral_angle_d16.9765234
X-RAY DIFFRACTIONf_chiral_restr0.0842394
X-RAY DIFFRACTIONf_plane_restr0.0082555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1312-3.16680.40221620.41073105X-RAY DIFFRACTION73
3.1668-3.20410.37882240.35424262X-RAY DIFFRACTION100
3.2041-3.24320.39182200.34034303X-RAY DIFFRACTION100
3.2432-3.28420.34852210.33334118X-RAY DIFFRACTION100
3.2842-3.32740.31742260.31244227X-RAY DIFFRACTION100
3.3274-3.3730.31272300.29984282X-RAY DIFFRACTION100
3.373-3.42120.34742150.27544205X-RAY DIFFRACTION100
3.4212-3.47230.28842250.26314201X-RAY DIFFRACTION100
3.4723-3.52650.25932300.254309X-RAY DIFFRACTION100
3.5265-3.58440.31172220.24124169X-RAY DIFFRACTION100
3.5844-3.64620.25962280.23594295X-RAY DIFFRACTION100
3.6462-3.71250.2822160.23444196X-RAY DIFFRACTION100
3.7125-3.78390.2612310.23514247X-RAY DIFFRACTION100
3.7839-3.86110.29972320.22664284X-RAY DIFFRACTION100
3.8611-3.94510.2552220.22114165X-RAY DIFFRACTION100
3.9451-4.03680.27492270.21084245X-RAY DIFFRACTION100
4.0368-4.13780.25542240.20524302X-RAY DIFFRACTION100
4.1378-4.24970.24912240.19624213X-RAY DIFFRACTION100
4.2497-4.37470.23012230.19594207X-RAY DIFFRACTION100
4.3747-4.51590.23992230.18184189X-RAY DIFFRACTION100
4.5159-4.67730.2142190.17334280X-RAY DIFFRACTION100
4.6773-4.86460.24122240.1864219X-RAY DIFFRACTION100
4.8646-5.0860.23042240.18844243X-RAY DIFFRACTION100
5.086-5.35410.21472210.18034272X-RAY DIFFRACTION100
5.3541-5.68950.21172220.1854222X-RAY DIFFRACTION100
5.6895-6.12870.24072240.18924246X-RAY DIFFRACTION100
6.1287-6.74540.2522170.19364232X-RAY DIFFRACTION100
6.7454-7.72110.23322190.21064267X-RAY DIFFRACTION100
7.7211-9.72630.18762250.18914217X-RAY DIFFRACTION100
9.7263-96.54370.25142230.21764220X-RAY DIFFRACTION99

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