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- PDB-4v0k: Crystal structure of the CrARL6DN in the GDP bound form -

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Basic information

Entry
Database: PDB / ID: 4v0k
TitleCrystal structure of the CrARL6DN in the GDP bound form
ComponentsARF-LIKE SMALL GTPASE
KeywordsHYDROLASE
Function / homology
Function and homology information


protein localization to cilium / axoneme / cilium assembly / vesicle-mediated transport / intracellular protein transport / GTPase activity / GTP binding / metal ion binding
Similarity search - Function
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
: / GUANOSINE-5'-DIPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.438 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARF-LIKE SMALL GTPASE
B: ARF-LIKE SMALL GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,62414
Polymers37,6132
Non-polymers2,01112
Water8,557475
1
A: ARF-LIKE SMALL GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9248
Polymers18,8071
Non-polymers1,1187
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARF-LIKE SMALL GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6996
Polymers18,8071
Non-polymers8935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.725, 65.725, 185.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ARF-LIKE SMALL GTPASE / ARL6


Mass: 18806.646 Da / Num. of mol.: 2 / Fragment: GTPASE, RESIDUES 16-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Plasmid: PEC-A-HT-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8JF99
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 3.14 Å3/Da / Density % sol: 60.84 % / Description: NONE
Crystal growDetails: 12% POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH7.5, 5MM CDCL2, 5MM MGCL2, 5MM NICL2, 5MM COCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 83301 / % possible obs: 96.2 % / Observed criterion σ(I): 1.8 / Redundancy: 8.8 % / Biso Wilson estimate: 17.55 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.8
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.8 / % possible all: 89.9

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Processing

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

Resolution: 1.438→48.504 Å / SU ML: 0.13 / σ(F): 1.92 / Phase error: 17.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 8105 5 %
Rwork0.1547 --
obs0.1562 83301 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.438→48.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 66 475 2976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072552
X-RAY DIFFRACTIONf_angle_d1.3013482
X-RAY DIFFRACTIONf_dihedral_angle_d14.157940
X-RAY DIFFRACTIONf_chiral_restr0.08397
X-RAY DIFFRACTIONf_plane_restr0.005440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4375-1.45380.28742500.28614652X-RAY DIFFRACTION91
1.4538-1.4710.28582700.26955179X-RAY DIFFRACTION100
1.471-1.48890.26262740.25075163X-RAY DIFFRACTION100
1.4889-1.50770.29532700.25295093X-RAY DIFFRACTION100
1.5077-1.52760.28332740.24375238X-RAY DIFFRACTION100
1.5276-1.54850.26792740.2255100X-RAY DIFFRACTION100
1.5485-1.57060.26072670.21815162X-RAY DIFFRACTION100
1.5706-1.59410.21192670.20245137X-RAY DIFFRACTION100
1.5941-1.6190.22962650.18855193X-RAY DIFFRACTION100
1.619-1.64550.22062730.17825196X-RAY DIFFRACTION100
1.6455-1.67390.17612710.16155168X-RAY DIFFRACTION100
1.6739-1.70430.19312650.14955110X-RAY DIFFRACTION100
1.7043-1.73710.1692670.14935207X-RAY DIFFRACTION100
1.7371-1.77260.18192690.14035174X-RAY DIFFRACTION100
1.7726-1.81110.18742650.13635148X-RAY DIFFRACTION100
1.8111-1.85330.1762720.13165139X-RAY DIFFRACTION100
1.8533-1.89960.18252660.13035155X-RAY DIFFRACTION100
1.8996-1.9510.16042720.12855168X-RAY DIFFRACTION100
1.951-2.00840.15732750.12315168X-RAY DIFFRACTION100
2.0084-2.07320.18122770.12425161X-RAY DIFFRACTION100
2.0732-2.14730.15822720.12515147X-RAY DIFFRACTION100
2.1473-2.23330.16182680.12945176X-RAY DIFFRACTION100
2.2333-2.33490.17832690.13685154X-RAY DIFFRACTION100
2.3349-2.4580.1922760.13275146X-RAY DIFFRACTION100
2.458-2.6120.18182730.14465172X-RAY DIFFRACTION100
2.612-2.81370.18422720.15375158X-RAY DIFFRACTION100
2.8137-3.09680.17342750.16045155X-RAY DIFFRACTION100
3.0968-3.54480.19442750.14875159X-RAY DIFFRACTION100
3.5448-4.46560.15022720.14345153X-RAY DIFFRACTION100
4.4656-48.53150.18292700.18065156X-RAY DIFFRACTION100

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