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- PDB-2x77: Crystal Structure of Leishmania major ADP ribosylation factor-like 1. -

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Basic information

Entry
Database: PDB / ID: 2x77
TitleCrystal Structure of Leishmania major ADP ribosylation factor-like 1.
ComponentsADP-RIBOSYLATION FACTOR
KeywordsGTP-BINDING PROTEIN / SMALL GTPASE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


protein targeting to lysosome / ciliary plasm / nuclear lumen / regulation of endocytosis / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / GTPase activity / GTP binding / Golgi apparatus ...protein targeting to lysosome / ciliary plasm / nuclear lumen / regulation of endocytosis / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / GTPase activity / GTP binding / Golgi apparatus / 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
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor-like protein 1
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFleming, J.R. / Dawson, A. / Hunter, W.N.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2010
Title: Crystal Structure of Leishmania Major Adp Ribosylation Factor-Like 1 and a Classification of Related Gtpase Family Members in This Kinetoplastid.
Authors: Fleming, J.R. / Dawson, A. / Hunter, W.N.
History
DepositionFeb 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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 / 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-RIBOSYLATION FACTOR
B: ADP-RIBOSYLATION FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9516
Polymers42,0162
Non-polymers9354
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-35.4 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.286, 78.944, 58.034
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ADP-RIBOSYLATION FACTOR / ADP RIBOSYLATION FACTOR-LIKE 1


Mass: 21007.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DISULPHIDE LINK BETWEEN C83A AND C83B / Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Plasmid: PET15BTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q4QEJ1
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.64 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROPS OF 0.75 UL PROTEIN SOLUTION, 0.75 UL 75 MM CALCIUM ACETATE, 17 % PEG 3350.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98137
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98137 Å / Relative weight: 1
ReflectionResolution: 2.1→78.1 Å / Num. obs: 18516 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOZ

1moz


Resolution: 2.1→78.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.817 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 49 TO 54 AND 74 TO 82 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.28682 947 5.1 %RANDOM
Rwork0.21389 ---
obs0.21773 17566 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.52 Å2
2--2.86 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→78.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 58 81 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9993916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42124.252127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50115514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4361521
X-RAY DIFFRACTIONr_chiral_restr0.1190.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022095
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9341.51728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66322785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2931148
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.514.51126
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 66 -
Rwork0.277 1292 -
obs--99.05 %

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