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- PDB-6a8d: Crystal Structure of Chlamydomonas reinhardtii ARF -

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Basic information

Entry
Database: PDB / ID: 6a8d
TitleCrystal Structure of Chlamydomonas reinhardtii ARF
ComponentsARF/SAR superfamily small monomeric GTP binding protein
KeywordsPROTEIN TRANSPORT / Chlamydomonas reinhardtii / ARF / ADP-ribosylation factor
Function / homology
Function and homology information


vesicle-mediated transport / intracellular protein transport / GTPase activity / GTP binding / metal ion 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 / Arf
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsKumari, S. / Goel, M. / Kateriya, S. / Sharma, P.
Funding support India, 1items
OrganizationGrant numberCountry
India
Citation
Journal: To Be Published
Title: Crystal structure of Chlamydomonas reinhardtii Arf
Authors: Kumari, S. / Sharma, P. / Kateriya, S. / Goel, M.
#1: Journal: J. Phycol. / Year: 2014
Title: Cellular organelles facilitate dimerization of a newly identified Arf from Chlamydomonas reinhardtii
Authors: Ranjan, P. / Kashyap, R.S. / Goel, M. / Veetil, S.K. / Kateriya, S.
History
DepositionJul 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARF/SAR superfamily small monomeric GTP binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3814
Polymers21,8171
Non-polymers5643
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-16 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.818, 44.244, 113.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ARF/SAR superfamily small monomeric GTP binding protein / Arf


Mass: 21817.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CGL49, CHLRE_12g487850v5, CHLREDRAFT_78189 / Plasmid: pET21a / Production host: Escherichia coli BL21 (DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: A8ILA3
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.63 Å3/Da / Density % sol: 53.23 % / Description: ROD SHAPED CRYSTAL
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG8000, 200mM Ammonium Sulphate / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→56.75 Å / Num. obs: 9681 / % possible obs: 98.8 % / Redundancy: 10.7 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.1 / Χ2: 1.291 / Net I/σ(I): 35.71
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.44 / CC1/2: 0.887 / Rpim(I) all: 0.259 / Rrim(I) all: 0.734 / Χ2: 1.008 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUR, 1RRG, 3AQ4, 5A1U

1hur

1rrg

3aq4

5a1u


Resolution: 2.34→56.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.438 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26563 448 4.7 %RANDOM
Rwork0.22037 ---
obs0.22251 9171 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20 Å2
2--4.48 Å20 Å2
3----3.99 Å2
Refinement stepCycle: 1 / Resolution: 2.34→56.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 34 46 1490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191488
X-RAY DIFFRACTIONr_bond_other_d0.0020.021345
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9562027
X-RAY DIFFRACTIONr_angle_other_deg1.13433095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8875182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66423.53865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.1915239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.912159
X-RAY DIFFRACTIONr_chiral_restr0.1290.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021646
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7925.857728
X-RAY DIFFRACTIONr_mcbond_other4.7935.85727
X-RAY DIFFRACTIONr_mcangle_it7.2348.766910
X-RAY DIFFRACTIONr_mcangle_other7.238.773911
X-RAY DIFFRACTIONr_scbond_it4.8516.144760
X-RAY DIFFRACTIONr_scbond_other4.8576.148748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1099.0811099
X-RAY DIFFRACTIONr_long_range_B_refined9.73468.0031722
X-RAY DIFFRACTIONr_long_range_B_other9.73767.8731702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.345→2.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 35 -
Rwork0.322 598 -
obs--90.04 %

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