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- PDB-4eyy: Crystal Structure of the IcmR-IcmQ complex from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 4eyy
TitleCrystal Structure of the IcmR-IcmQ complex from Legionella pneumophila
Components
  • IcmQ
  • IcmR
KeywordsPROTEIN BINDING / Protein heterodimer / ADPRT-like fold / NAD-binding domain
Function / homology
Function and homology information


Dot/Icm secretion system IcmQ, C-terminal domain / : / IcmR, middle region / ADP-ribosylation fold / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Legionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsFarelli, J.D. / Gumbart, J. / Akey, I.V. / Amyot, W. / Hempstead, A.D. / Head, J.F. / McKnight, C.J. / Isberg, R.R. / Akey, C.W.
CitationJournal: Structure / Year: 2013
Title: IcmQ in the Type 4b secretion system contains an NAD+ binding domain.
Authors: Farelli, J.D. / Gumbart, J.C. / Akey, I.V. / Hempstead, A. / Amyot, W. / Head, J.F. / McKnight, C.J. / Isberg, R.R. / Akey, C.W.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
R: IcmR
Q: IcmQ


Theoretical massNumber of molelcules
Total (without water)34,4762
Polymers34,4762
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-21 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.948, 113.411, 49.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11R-214-

HOH

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Components

#1: Protein IcmR


Mass: 12961.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: icmR, lpg0443 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (REP4) / References: UniProt: Q5ZYC9
#2: Protein IcmQ


Mass: 21514.600 Da / Num. of mol.: 1 / Mutation: K57Q, K59Q, R67Q, R71Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: icmQ, LPC_2899 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (REP4) / References: UniProt: A5IHF0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.856.15
2
Crystal growTemperature: 294 K
Details: Protein concentration 8 mg/ml. Selenomethionine-incorporated protein for SAD phasing. 1:1 ratio of protein to 24% PEG 1500, 0.1 M sodium citrate pH 5.9, 1 mM DTT and 1% ethylene glycol. ...Details: Protein concentration 8 mg/ml. Selenomethionine-incorporated protein for SAD phasing. 1:1 ratio of protein to 24% PEG 1500, 0.1 M sodium citrate pH 5.9, 1 mM DTT and 1% ethylene glycol. Cryoprotected in mother liquor + 30% ethylene glycol and frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 294K
PH range: 5.9; 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X2510.9789
SYNCHROTRONNSLS X2521
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 1, 2010
ADSC QUANTUM 3152CCDFeb 1, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
211
ReflectionResolution: 2.4→19.754 Å / Num. obs: 15596 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 45.63 Å2 / Rmerge(I) obs: 0.208 / Rsym value: 0.054 / Net I/σ(I): 20.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 5.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.75 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 1560 10 %
Rwork0.217 --
obs0.222 15596 99.1 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.51 Å2 / ksol: 0.17 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.0117 Å20 Å2-0 Å2
2--3.2307 Å20 Å2
3----18.2423 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 0 118 2038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171943
X-RAY DIFFRACTIONf_angle_d1.7212621
X-RAY DIFFRACTIONf_dihedral_angle_d18.992737
X-RAY DIFFRACTIONf_chiral_restr0.162308
X-RAY DIFFRACTIONf_plane_restr0.006335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47740.33241390.29481254X-RAY DIFFRACTION99
2.4774-2.56570.36281410.28121259X-RAY DIFFRACTION99
2.5657-2.66820.33931390.28291249X-RAY DIFFRACTION99
2.6682-2.78930.3021380.25091252X-RAY DIFFRACTION100
2.7893-2.9360.29771420.25361274X-RAY DIFFRACTION100
2.936-3.11920.28021410.25271267X-RAY DIFFRACTION100
3.1192-3.3590.31781420.24951275X-RAY DIFFRACTION100
3.359-3.6950.27981430.22391287X-RAY DIFFRACTION100
3.695-4.22520.22441440.19671299X-RAY DIFFRACTION100
4.2252-5.30610.20121470.18091318X-RAY DIFFRACTION100
5.3061-19.75430.24311440.17971302X-RAY DIFFRACTION94

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