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- PDB-1xsz: The structure of RalF -

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Basic information

Entry
Database: PDB / ID: 1xsz
TitleThe structure of RalF
Componentsguanine nucleotide exchange protein
KeywordsSIGNALING PROTEIN / Arf guanine nucleotide exchange factor
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 / MIR / Resolution: 1.41 Å
AuthorsAmor, J.C. / Swails, J. / Roy, C.R. / Nagai, H. / Ingmundson, A. / Cheng, X. / Kahn, R.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The structure of RalF, an ADP-ribosylation factor guanine nucleotide exchange factor from Legionella pneumophila, reveals the presence of a cap over the active site
Authors: Amor, J.C. / Swails, J. / Zhu, X. / Roy, C.R. / Nagai, H. / Ingmundson, A. / Cheng, X. / Kahn, R.A.
History
DepositionOct 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: guanine nucleotide exchange protein
B: guanine nucleotide exchange protein


Theoretical massNumber of molelcules
Total (without water)79,9222
Polymers79,9222
Non-polymers00
Water19,7081094
1
A: guanine nucleotide exchange protein


Theoretical massNumber of molelcules
Total (without water)39,9611
Polymers39,9611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: guanine nucleotide exchange protein


Theoretical massNumber of molelcules
Total (without water)39,9611
Polymers39,9611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.559, 84.559, 110.175
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein guanine nucleotide exchange protein


Mass: 39960.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Plasmid: pHis-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RT31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.41→40 Å / Num. all: 171080 / Num. obs: 171080 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.4
Reflection shellResolution: 1.41→1.45 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.5 / Num. unique all: 12087 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.41→40 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1161140.22 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 16995 9.9 %RANDOM
Rwork0.2018 ---
all-171080 --
obs-171080 99.5 %-
Solvent computationBsol: 46.4095 Å2 / ksol: 0.365522 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.782 Å20.202 Å20 Å2
2---0.782 Å20 Å2
3---1.564 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.41→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 0 1094 7160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.0851.5
X-RAY DIFFRACTIONc_mcangle_it1.7092
X-RAY DIFFRACTIONc_scbond_it1.9512
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 1.41→1.45 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 1627 10.3 %
Rwork0.278 14137 -
obs-12087 99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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