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- PDB-4bas: Structure of the Arl6 BBS3 Small GTPase from Trypanosoma brucei w... -

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Basic information

Entry
Database: PDB / ID: 4bas
TitleStructure of the Arl6 BBS3 Small GTPase from Trypanosoma brucei with bound nucleotide analogue GppNp
ComponentsADP-RIBOSYLATION FACTOR, PUTATIVE (SMALL GTPASE, PUTATIVE)
KeywordsHYDROLASE
Function / homology
Function and homology information


GTPase activity / GTP binding / metal ion binding / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / ADP-ribosylation factor, putative
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHemsworth, G.R. / Price, H.P. / Smith, D.F. / Wilson, K.S.
CitationJournal: Protein Sci. / Year: 2013
Title: Crystal Structure of the Small Gtpase Arl6/Bbs3 from Trypanosomabrucei.
Authors: Hemsworth, G.R. / Price, H.P. / Smith, D.F. / Wilson, K.S.
History
DepositionSep 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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.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.value / _struct_conn.pdbx_dist_value / _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_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_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, PUTATIVE (SMALL GTPASE, PUTATIVE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5775
Polymers21,8381
Non-polymers7394
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ADP-RIBOSYLATION FACTOR, PUTATIVE (SMALL GTPASE, PUTATIVE)
hetero molecules

A: ADP-RIBOSYLATION FACTOR, PUTATIVE (SMALL GTPASE, PUTATIVE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,15310
Polymers43,6762
Non-polymers1,4778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area4460 Å2
ΔGint-101.6 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.920, 70.920, 80.928
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2084-

HOH

21A-2085-

HOH

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Components

#1: Protein ADP-RIBOSYLATION FACTOR, PUTATIVE (SMALL GTPASE, PUTATIVE) / ADP-RIBOSYLATION FACTOR-LIKE


Mass: 21837.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI TREU927 (eukaryote) / Plasmid: PET-YSBLLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9ZVV9, small monomeric GTPase
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.2 M CSCL, 2.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 4, 2011 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→48.92 Å / Num. obs: 15861 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15
Reflection shellResolution: 2→2.11 Å / Redundancy: 11 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0005refinement
XDSdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H57

2h57


Resolution: 2→61.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.926 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24783 796 5 %RANDOM
Rwork0.18345 ---
obs0.18658 15009 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.531 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.73 Å20 Å2
2--1.45 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2→61.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 43 96 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021387
X-RAY DIFFRACTIONr_bond_other_d0.0010.02895
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9781888
X-RAY DIFFRACTIONr_angle_other_deg0.88932187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90424.21157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28815223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.812156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.235 58 -
Rwork0.229 1043 -
obs--99.91 %

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