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- PDB-4d7r: Crystal structure of a chimeric protein with the Sec7 domain of R... -

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Basic information

Entry
Database: PDB / ID: 4d7r
TitleCrystal structure of a chimeric protein with the Sec7 domain of Rickettsia prowazekii RalF and the capping domain of Legionella pneumophila RalF
ComponentsPROLINE/BETAINE TRANSPORTER, RALF
KeywordsSIGNALING PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR / BACTERIAL PATHOGENS / CHIMERIC 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
: / RalF / PROTEIN TRANSPORT PROTEIN SEC7 (Sec7)
Similarity search - Component
Biological speciesRickettsia prowazekii str. Madrid E (bacteria)
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFolly-Klan, M. / Sancerne, B. / Alix, E. / Roy, C.R. / Cherfils, J. / Campanacci, V.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: On the Use of Legionella/Rickettsia Chimeras to Investigate the Structure and Regulation of Rickettsia Effector Ralf.
Authors: Folly-Klan, M. / Sancerne, B. / Alix, E. / Roy, C.R. / Cherfils, J. / Campanacci, V.
History
DepositionNov 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROLINE/BETAINE TRANSPORTER, RALF


Theoretical massNumber of molelcules
Total (without water)46,0031
Polymers46,0031
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.690, 94.840, 47.140
Angle α, β, γ (deg.)90.00, 111.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROLINE/BETAINE TRANSPORTER, RALF


Mass: 46002.805 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-195,195-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii str. Madrid E (bacteria), (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: M9TGB4, UniProt: Q8RT31, UniProt: Q9ZDF5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A CHIMERIC PROTEIN CONTAINING RESIDUES 2 TO 195 FROM RICKETTSIA PROWAZEKII RALF (M9TGB4) ...THIS IS A CHIMERIC PROTEIN CONTAINING RESIDUES 2 TO 195 FROM RICKETTSIA PROWAZEKII RALF (M9TGB4) AND RESIDUES 198 TO 374 FROM LEGIONELLA PNEUMOPHILA RALF (Q8RT31). THE N- TERMINAL SEQUENCE MSYYHHHHHHLESTSLYKKAGLENLYFQG CORRESPONDS TO THE 6-HISTIDINE TAG AND TEV PROTEASE CLEAVAGE SITE.

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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: 2.34 Å3/Da / Density % sol: 47.5 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM CHLORIDE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→43.79 Å / Num. obs: 33357 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 3.28 % / Biso Wilson estimate: 22.34 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.1
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.1 / % possible all: 92.6

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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: 1.8→24.01 Å / Cor.coef. Fo:Fc: 0.9522 / Cor.coef. Fo:Fc free: 0.9225 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 1678 5.07 %RANDOM
Rwork0.1784 ---
obs0.1806 33125 95.9 %-
Displacement parametersBiso mean: 26.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.8597 Å20 Å22.117 Å2
2--2.2558 Å20 Å2
3----4.1155 Å2
Refine analyzeLuzzati coordinate error obs: 0.238 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 0 418 3288
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012985HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024036HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1073SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes418HARMONIC5
X-RAY DIFFRACTIONt_it2985HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion17.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion397SEMIHARMONIC5
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_contact3874SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2205 143 5.17 %
Rwork0.2008 2623 -
all0.2018 2766 -
obs--95.9 %
Refinement TLS params.Method: refined / Origin x: 13.5607 Å / Origin y: -0.283 Å / Origin z: 4.4119 Å
111213212223313233
T-0.0411 Å2-0.0043 Å2-0.0373 Å2--0.0728 Å20.0096 Å2---0.0373 Å2
L0.393 °20.0164 °20.0724 °2-1.1146 °20.3482 °2--0.688 °2
S0.0128 Å °-0.0083 Å °0.0183 Å °-0.0444 Å °-0.0391 Å °0.0185 Å °-0.0705 Å °-0.0599 Å °0.0263 Å °
Refinement TLS groupSelection details: { A|* }

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