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- PDB-4d7q: Crystal structure of a chimeric protein with the Sec7 domain of L... -

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Basic information

Entry
Database: PDB / ID: 4d7q
TitleCrystal structure of a chimeric protein with the Sec7 domain of Legionella pneumophila RalF and the capping domain of Rickettsia prowazekii RalF
ComponentsRALF, PROLINE/BETAINE TRANSPORTERRalph
KeywordsSIGNALING PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR / BACTERIAL PATHOGENS
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
NITRATE ION / DI(HYDROXYETHYL)ETHER / : / RalF
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
RICKETTSIA PROWAZEKII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Jan 21, 2015Group: Atomic model / Derived calculations / Other
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
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 / 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, PROLINE/BETAINE TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3979
Polymers40,5161
Non-polymers8818
Water4,828268
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.310, 77.440, 119.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RALF, PROLINE/BETAINE TRANSPORTER / Ralph


Mass: 40515.672 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria), (gene. exp.) RICKETTSIA PROWAZEKII (bacteria)
Strain: PHILADELPHIA STRAIN 1, MADRID E / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q8RT31, UniProt: M9TGB4

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Non-polymers , 5 types, 276 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS IS A CHIMERIC PROTEIN CONTAINING RESIDUES 2 TO 197 FROM LEGIONELLA PNEUMOPHILA RALF (Q8RT31) ...THIS IS A CHIMERIC PROTEIN CONTAINING RESIDUES 2 TO 197 FROM LEGIONELLA PNEUMOPHILA RALF (Q8RT31) AND RESIDUES 196 TO 344 FROM RICKETTSIA PROWAZEKII RALF (M9TG84). THE N- TERMINAL SEQUENCE MKHHHHH CORRESPONDS TO THE 6-HISTIDINE TAG. THE D160Y MUTATION IS A CLONING ARTEFACT.

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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: 2.38 Å3/Da / Density % sol: 48.26 % / Description: NONE
Crystal growpH: 7.3
Details: 0.2 M POTASSIUM NITRATE, 0.1 M HEPES PH 6.8-7.8, 15-25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→38.72 Å / Num. obs: 25893 / % possible obs: 99.4 % / Observed criterion σ(I): 1.4 / Redundancy: 4.38 % / Biso Wilson estimate: 32.41 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.07
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.47 / % possible all: 98.7

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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: 2→38.72 Å / Cor.coef. Fo:Fc: 0.9543 / Cor.coef. Fo:Fc free: 0.9381 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1314 5.08 %RANDOM
Rwork0.1752 ---
obs0.1773 25873 99.58 %-
Displacement parametersBiso mean: 35.13 Å2
Baniso -1Baniso -2Baniso -3
1-2.4526 Å20 Å20 Å2
2---1.1535 Å20 Å2
3----1.2991 Å2
Refine analyzeLuzzati coordinate error obs: 0.211 Å
Refinement stepCycle: LAST / Resolution: 2→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 57 268 3137
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013004HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064090HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1094SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes400HARMONIC5
X-RAY DIFFRACTIONt_it3004HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion17.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion371SEMIHARMONIC5
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_contact3724SEMIHARMONIC4
LS refinement shellResolution: 2→2.08 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2744 144 5.04 %
Rwork0.2199 2711 -
all0.2225 2855 -
obs--99.58 %
Refinement TLS params.Method: refined / Origin x: 13.356 Å / Origin y: 0.2013 Å / Origin z: 12.7447 Å
111213212223313233
T-0.0314 Å2-0.0022 Å20.0001 Å2--0.0488 Å20.0054 Å2---0.0394 Å2
L0.321 °20.0318 °20.1201 °2-0.4708 °2-0.1703 °2--0.6562 °2
S-0.0117 Å °-0.0396 Å °-0.0148 Å °0.0602 Å °0.0071 Å °-0.04 Å °0.0659 Å °-0.035 Å °0.0046 Å °

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