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- PDB-2h17: Structure of human ADP-ribosylation factor-like 5 (ARL5) -

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Basic information

Entry
Database: PDB / ID: 2h17
TitleStructure of human ADP-ribosylation factor-like 5 (ARL5)
ComponentsADP-ribosylation factor-like protein 5A
KeywordsTRANSPORT PROTEIN / GDP / GTPASE / MEMBRANE TRAFFICKING / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


protein localization to Golgi membrane / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / GTPase activity / GTP binding
Similarity search - Function
Small GTPase superfamily, ARF type / 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 ...Small GTPase superfamily, ARF type / 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
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor-like protein 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRabeh, W.M. / Tempel, W. / Yaniw, D. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of human ADP-ribosylation factor-like 5 (ARL5)
Authors: Rabeh, W.M. / Tempel, W. / Yaniw, D. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 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 / Structure summary / Category: software / struct
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 / _struct.title
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 / 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 / _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 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ACCORDING TO AUTHORS, THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor-like protein 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0415
Polymers20,5971
Non-polymers4434
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.047, 48.772, 85.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsnot known

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Components

#1: Protein ADP-ribosylation factor-like protein 5A


Mass: 20597.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARL5A, ARFLP5, ARL5 / Plasmid: p28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y689
#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: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0M sodium formate, 0.1M BTP, pH 7.0, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.7→28.72 Å / Num. obs: 18505 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Χ2: 1.008 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
1.7-1.7697.65.60.47517770.713
1.76-1.8398.66.80.35118080.715
1.83-1.9198.77.10.28718040.937
1.91-2.0298.97.20.19618331.007
2.02-2.1498.67.20.12618171.053
2.14-2.3199.47.10.09718561.107
2.31-2.5499.37.20.06218320.916
2.54-2.9199.47.10.0518701.002
2.91-3.6699.770.03419081.172
3.66-3098.76.50.02820001.363

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å28.82 Å
Translation2.5 Å28.82 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ARP/wARPmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1z6y

1z6y


Resolution: 1.7→28.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.179 / SU B: 2.045 / SU ML: 0.07 / ESU R: 0.111 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 938 5.09 %random
Rwork0.1856 ---
all0.188 ---
obs-18430 98.889 %-
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: 17.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 31 64 1409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221374
X-RAY DIFFRACTIONr_bond_other_d0.0020.02896
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9631880
X-RAY DIFFRACTIONr_angle_other_deg1.05232209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20524.75461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12215252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.392157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_nbd_refined0.2130.2250
X-RAY DIFFRACTIONr_nbd_other0.2060.2932
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2684
X-RAY DIFFRACTIONr_nbtor_other0.0770.2704
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.214
X-RAY DIFFRACTIONr_mcbond_it3.1062901
X-RAY DIFFRACTIONr_mcbond_other0.7282335
X-RAY DIFFRACTIONr_mcangle_it3.72331341
X-RAY DIFFRACTIONr_scbond_it3.2042624
X-RAY DIFFRACTIONr_scangle_it4.8223531
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 (%)
1.7-1.7440.303680.25212280.255133796.933
1.744-1.7920.254730.21912390.221132199.319
1.792-1.8430.296690.19911880.204127698.511
1.843-1.90.241660.19411450.197123697.977
1.9-1.9620.249750.19711370.201123098.537
1.962-2.0310.205550.17811000.18116798.972
2.031-2.1070.213680.16910350.172110899.549
2.107-2.1920.228430.16410610.166111399.191
2.192-2.2890.217610.1789700.18104898.378
2.289-2.40.203450.1689440.1799799.198
2.4-2.5290.208430.169100.16295899.478
2.529-2.6820.246490.1948590.19791299.561
2.682-2.8650.237460.1918230.19487499.428
2.865-3.0920.206390.1937620.19380499.627
3.092-3.3840.251400.1857020.18974399.865
3.384-3.7770.277210.176610.17368499.708
3.777-4.350.182240.1655890.16661599.675
4.35-5.30.173310.1674870.16852299.234
5.3-7.3810.243130.2484060.24842099.762
7.381-300.31990.2362460.23927293.75

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