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- PDB-2h57: Crystal structure of human ADP-ribosylation factor-like 6 -

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Basic information

Entry
Database: PDB / ID: 2h57
TitleCrystal structure of human ADP-ribosylation factor-like 6
ComponentsADP-ribosylation factor-like protein 6
KeywordsTRANSPORT PROTEIN / GTP / GTPASE / MEMBRANE TRAFFICKING / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


protein transport from ciliary membrane to plasma membrane / protein localization to non-motile cilium / retina layer formation / melanosome transport / axonemal microtubule / BBSome-mediated cargo-targeting to cilium / membrane coat / protein localization to cilium / regulation of smoothened signaling pathway / determination of left/right symmetry ...protein transport from ciliary membrane to plasma membrane / protein localization to non-motile cilium / retina layer formation / melanosome transport / axonemal microtubule / BBSome-mediated cargo-targeting to cilium / membrane coat / protein localization to cilium / regulation of smoothened signaling pathway / determination of left/right symmetry / protein targeting to membrane / fat cell differentiation / axoneme / protein polymerization / cilium assembly / vesicle-mediated transport / visual perception / intracellular protein transport / brain development / phospholipid binding / cilium / Wnt signaling pathway / GTPase activity / GTP binding / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor-like protein 6 / small GTPase Arf family profile. / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / 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 / ADP-ribosylation factor-like protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, J. / Shen, Y. / Tempel, W. / Landry, R. / Lew, J. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Lew, J. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of human ADP-ribosylation factor-like 6 (CASP Target)
Authors: Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Lew, J. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_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.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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAINS. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAINS. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor-like protein 6
B: ADP-ribosylation factor-like protein 6
C: ADP-ribosylation factor-like protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,20118
Polymers64,5593
Non-polymers1,64215
Water2,396133
1
A: ADP-ribosylation factor-like protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0677
Polymers21,5201
Non-polymers5476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylation factor-like protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0676
Polymers21,5201
Non-polymers5475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADP-ribosylation factor-like protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0675
Polymers21,5201
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.058, 134.885, 63.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsnot known

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Components

#1: Protein ADP-ribosylation factor-like protein 6 / Bardet-Biedl syndrome 3 protein


Mass: 21519.637 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL6 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: Q9H0F7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.1 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate, pH 5.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 46561 / % possible obs: 97.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.043 / Χ2: 1.314 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2-2.0796.25.20.59944831.09
2.07-2.1596.45.30.44345321.151
2.15-2.25975.30.32545461.22
2.25-2.3797.35.30.23545721.269
2.37-2.5297.75.30.17345941.341
2.52-2.7198.25.30.12246321.414
2.71-2.9998.45.30.07846811.521
2.99-3.4299.15.30.04547261.567
3.42-4.3199.35.30.02748011.414
4.31-3099.35.10.01949941.125

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1zd9, 2H16

1zd9

2h16


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.203 / SU B: 4.096 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 1777 3.821 %thin shells
Rwork0.2059 ---
all0.207 ---
obs0.20749 46505 97.889 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.198 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2--2.829 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 108 133 4159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224103
X-RAY DIFFRACTIONr_bond_other_d0.0020.022692
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9835595
X-RAY DIFFRACTIONr_angle_other_deg1.03936631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77224.942172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52715715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9321517
X-RAY DIFFRACTIONr_chiral_restr0.080.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02768
X-RAY DIFFRACTIONr_nbd_refined0.1960.2751
X-RAY DIFFRACTIONr_nbd_other0.1910.22774
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21948
X-RAY DIFFRACTIONr_nbtor_other0.0790.22074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2172
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0670.25
X-RAY DIFFRACTIONr_mcbond_it2.5422584
X-RAY DIFFRACTIONr_mcbond_other0.5921014
X-RAY DIFFRACTIONr_mcangle_it3.69934047
X-RAY DIFFRACTIONr_scbond_it2.27421770
X-RAY DIFFRACTIONr_scangle_it3.10231539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2-2.05200.28333030.283344495.906
2.052-2.10800.26332300.263335896.188
2.108-2.1680.322930.25528720.26327296.73
2.168-2.23500.2430850.24318696.83
2.235-2.3080.2412540.23127420.232307897.336
2.308-2.38800.22729260.227300297.468
2.388-2.4780.2972140.22125920.227287497.634
2.478-2.57800.22727500.227281397.76
2.578-2.6920.2641990.22524280.228267498.242
2.692-2.8220.2561820.2123430.214256098.633
2.822-2.97300.21124070.211245198.205
2.973-3.1520.2791430.20621550.211231699.223
3.152-3.3670.2261200.20520650.207220898.958
3.367-3.63300.20120180.201203599.165
3.633-3.9740.249940.18217970.185190299.422
3.974-4.4330.172820.16916330.169172499.478
4.433-5.10.218690.16314700.165154799.483
5.1-6.2020.296400.21212810.215132499.773
6.202-8.5890.238590.22510020.2261061100
8.589-300.228280.2046290.20567996.76

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