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- PDB-3fxd: Crystal structure of interacting domains of IcmR and IcmQ -

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Basic information

Entry
Database: PDB / ID: 3fxd
TitleCrystal structure of interacting domains of IcmR and IcmQ
Components
  • Protein IcmQ
  • Protein IcmR
KeywordsUNKNOWN FUNCTION / 4 helix bundle / helix-turn-helix
Function / homology
Function and homology information


: / IcmR, middle region / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesLegionella pneumophila (bacteria)
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRaychaudhury, S. / Akey, C.W. / Head, J.F.
CitationJournal: Structure / Year: 2009
Title: Structure and Function of Interacting IcmR-IcmQ Domains from a Type IVb Secretion System in Legionella pneumophila.
Authors: Raychaudhury, S. / Farelli, J.D. / Montminy, T.P. / Matthews, M. / Menetret, J.F. / Dumenil, G. / Roy, C.R. / Head, J.F. / Isberg, R.R. / Akey, C.W.
History
DepositionJan 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein IcmQ
B: Protein IcmR
C: Protein IcmQ
D: Protein IcmR


Theoretical massNumber of molelcules
Total (without water)28,6114
Polymers28,6114
Non-polymers00
Water1,60389
1
A: Protein IcmQ
B: Protein IcmR


Theoretical massNumber of molelcules
Total (without water)14,3052
Polymers14,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-19.9 kcal/mol
Surface area6260 Å2
MethodPISA
2
C: Protein IcmQ
D: Protein IcmR


Theoretical massNumber of molelcules
Total (without water)14,3052
Polymers14,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-20.9 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.56, 95.56, 56.01
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein IcmQ


Mass: 6510.630 Da / Num. of mol.: 2 / Fragment: UNP residues 1-57
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: icmQ, LPC_2899 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: A5IHF0
#2: Protein Protein IcmR


Mass: 7794.728 Da / Num. of mol.: 2 / Fragment: UNP residues 23-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia-1 / DSM 7513 / Gene: icmR, lpg0443 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: Q5ZYC9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100 mM Na acetate pH 4.7, 30% PEG 1500, 100 mM L-cysteine, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17193 / Num. obs: 17193 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5 / Num. unique all: 1697 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
EPMRphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FXE

3fxe


Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1301 -random
Rwork0.21 ---
all0.21 16698 --
obs0.21 16698 97.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 89 1735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.98
X-RAY DIFFRACTIONc_bond_d0.022

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