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- PDB-4c7p: Crystal structure of Legionella pneumophila RalF F255K mutant -

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Basic information

Entry
Database: PDB / ID: 4c7p
TitleCrystal structure of Legionella pneumophila RalF F255K mutant
ComponentsRALF
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity
Similarity search - Function
sec7 domains / RalF, C-terminal domain superfamily / RalF, C-terminal Sec-7 capping domain / RalF C-terminal Sec-7 capping domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily ...sec7 domains / RalF, C-terminal domain superfamily / RalF, C-terminal Sec-7 capping domain / RalF C-terminal Sec-7 capping domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFolly-Klan, M. / Alix, E. / Stalder, D. / Ray, P. / Duarte, L.V. / Delprato, A. / Zeghouf, M. / Antonny, B. / Campanacci, V. / Roy, C.R. / Cherfils, J.
CitationJournal: Plos Pathog. / Year: 2013
Title: A Novel Membrane Sensor Controls the Localization and Arfgef Activity of Bacterial Ralf.
Authors: Folly-Klan, M. / Alix, E. / Stalder, D. / Ray, P. / Duarte, L.V. / Delprato, A. / Zeghouf, M. / Antonny, B. / Campanacci, V. / Roy, C.R. / Cherfils, J.
History
DepositionSep 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 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 / 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 / _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

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Assembly

Deposited unit
A: RALF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6152
Polymers45,5231
Non-polymers921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.265, 78.265, 115.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RALF / GUANINE EXCHANGE FACTOR RALF


Mass: 45523.035 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA STRAIN 1 / Plasmid: PHIS1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q8RT31
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Sequence details6 HIS-TAG AND TEV PROTEASE CLEAVAGE SITE AT THE N-TERMINUS MUTATION AT POSITION 255 (F255K)

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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: 2.39 Å3/Da / Density % sol: 48.66 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 25% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→39.13 Å / Num. obs: 7973 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Biso Wilson estimate: 90.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XSZ

1xsz


Resolution: 3.1→39.13 Å / Cor.coef. Fo:Fc: 0.9445 / Cor.coef. Fo:Fc free: 0.9143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.514
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 751 9.73 %RANDOM
Rwork0.1977 ---
obs0.2059 7716 99.19 %-
Displacement parametersBiso mean: 116.76 Å2
Baniso -1Baniso -2Baniso -3
1--7.0397 Å20 Å20 Å2
2---7.0397 Å20 Å2
3---14.0795 Å2
Refine analyzeLuzzati coordinate error obs: 0.795 Å
Refinement stepCycle: LAST / Resolution: 3.1→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 6 0 2761
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012825HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.253822HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d998SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes393HARMONIC5
X-RAY DIFFRACTIONt_it2825HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion24.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3332SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.47 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2876 195 9.01 %
Rwork0.1925 1970 -
all0.2011 2165 -
obs--99.19 %
Refinement TLS params.Method: refined / Origin x: 1.1491 Å / Origin y: 33.1135 Å / Origin z: 1.6544 Å
111213212223313233
T-0.254 Å20.2089 Å2-0.0142 Å2--0.1597 Å2-0.0468 Å2---0.6919 Å2
L2.5233 °20.3509 °21.2072 °2-3.1067 °21.1652 °2--7.0775 °2
S-0.0498 Å °0.2002 Å °0.3527 Å °0.1098 Å °0.1544 Å °-0.0318 Å °0.2152 Å °0.317 Å °-0.1046 Å °
Refinement TLS groupSelection details: CHAIN A

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