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- PDB-1yzg: Structure of Human ADP-ribosylation factor-like 8 -

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Basic information

Entry
Database: PDB / ID: 1yzg
TitleStructure of Human ADP-ribosylation factor-like 8
ComponentsADP-ribosylation factor-like 8
KeywordsTRANSPORT PROTEIN / GDP-BINDING / MEMBRANE TRAFFICKING / Structural Genomics / PSI / Protein Structure Initiative / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein localization to Golgi membrane / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / GTP binding
Similarity search - Function
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor-like protein 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChoe, J. / Atanassova, A. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published / Year: 2005
Title: Structure of Human ADP-ribosylation factor-like 8
Authors: Atanassova, A. / Choe, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Bochkarev, A. / Park, H.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor-like 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8412
Polymers20,3981
Non-polymers4431
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.725, 48.137, 51.371
Angle α, β, γ (deg.)90.00, 103.45, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein ADP-ribosylation factor-like 8


Mass: 20397.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96KC2
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, Sodium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2005
RadiationMonochromator: CONFOCAL MAXFLUX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 12238 / Num. obs: 12238 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.077
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1220 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClear(MSC/RIGAKU)data reduction
AMoREphasing
REFMAC5.2refinement
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRF

1rrf


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.762 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27 617 5 %RANDOM
Rwork0.226 ---
all0.2261 12228 --
obs0.2261 11611 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.55 Å2
2---0.16 Å20 Å2
3---0.99 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 28 120 1489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221398
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9641899
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48124.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.474155
X-RAY DIFFRACTIONr_chiral_restr0.1090.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021010
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2701
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2932
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9091.5863
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40521346
X-RAY DIFFRACTIONr_scbond_it1.9733640
X-RAY DIFFRACTIONr_scangle_it2.794.5553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 36 -
Rwork0.244 846 -
obs-851 100 %

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