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- PDB-3fxe: Crystal structure of interacting domains of IcmR and IcmQ (seleno... -

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Basic information

Entry
Database: PDB / ID: 3fxe
TitleCrystal structure of interacting domains of IcmR and IcmQ (seleno-derivative)
Components
  • Protein IcmQ
  • Protein IcmR
KeywordsUNKNOWN FUNCTION / 4 helix bundle / helix-turn-helix / Se-Met
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 / MAD / Resolution: 2.2 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 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein IcmQ
B: Protein IcmR


Theoretical massNumber of molelcules
Total (without water)14,4172
Polymers14,4172
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-16.11 kcal/mol
Surface area5840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.09, 42.10, 78.92
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein IcmQ


Mass: 6557.525 Da / Num. of mol.: 1 / 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: 7859.662 Da / Num. of mol.: 1 / Fragment: UNP residues 23-95 / Mutation: L84M
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.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.64 %
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: X12C / Wavelength: 0.97950, 0.97976, 0.95003
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 10, 2004
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979761
30.950031
ReflectionResolution: 2.2→50 Å / Num. all: 10087 / Num. obs: 10087 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 18 / Num. unique all: 541 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 841 -random
Rwork0.23 ---
all0.23 10087 --
obs0.23 10087 99.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 0 33 836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.05
X-RAY DIFFRACTIONc_bond_d0.006

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