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- PDB-4bes: Crystal structure of the Legionella pneumophila FIC domain-contai... -

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Basic information

Entry
Database: PDB / ID: 4bes
TitleCrystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein in complex with cytidine monophosphate and phosphocholine
ComponentsPHOSPHOCHOLINE TRANSFERASE ANKX
KeywordsTRANSFERASE / PHOSPHOCHOLINATION / TYPE IV SECRETION SYSTEM EFFECTOR
Function / homology
Function and homology information


phosphocholine transferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / regulation of GTPase activity / host cell cytoplasm / extracellular region
Similarity search - Function
: / : / Phosphocholine transferase AnkX insertion domain / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...: / : / Phosphocholine transferase AnkX insertion domain / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHOCHOLINE / Phosphocholine transferase AnkX
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsCampanacci, V. / Mukherjee, S. / Roy, C.R. / Cherfils, J.
CitationJournal: Embo J. / Year: 2013
Title: Structure of the Legionella Effector Ankx Reveals the Mechanism of Phosphocholine Transfer by the Fic Domain.
Authors: Campanacci, V. / Mukherjee, S. / Roy, C.R. / Cherfils, J.
History
DepositionMar 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Dec 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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6856
Polymers54,8901
Non-polymers7965
Water97354
1
A: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules

A: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,37012
Polymers109,7792
Non-polymers1,59110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5540 Å2
ΔGint-111.1 kcal/mol
Surface area39460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.275, 122.304, 54.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PHOSPHOCHOLINE TRANSFERASE ANKX / PC TRANSFERASE / ANKYRIN REPEAT-CONTAINING PROTEIN X


Mass: 54889.660 Da / Num. of mol.: 1 / Fragment: FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q5ZXN6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPHOSPHOCHOLINE (PC): PRODUCED AFTER ADDITION OF CDP-CHOLINE CYTIDINE-5'-MONOPHOSPHATE (C5P): ...PHOSPHOCHOLINE (PC): PRODUCED AFTER ADDITION OF CDP-CHOLINE CYTIDINE-5'-MONOPHOSPHATE (C5P): PRODUCED AFTER ADDITION OF CDP-CHOLINE
Sequence detailsL247P (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: 2.43 Å3/Da / Density % sol: 49.45 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M AMMONIUM SULFATE, 30% PEG 5000 MME, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.54→43.1 Å / Num. obs: 19367 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 55.92 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.42
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8

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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 4BEP

4bep


Resolution: 2.54→43.1 Å / Cor.coef. Fo:Fc: 0.9243 / Cor.coef. Fo:Fc free: 0.8889 / SU R Cruickshank DPI: 0.504 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.511 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.292
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 1041 5.38 %RANDOM
Rwork0.2005 ---
obs0.2035 19367 99.71 %-
Displacement parametersBiso mean: 55.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.0811 Å20 Å20 Å2
2--10.5972 Å20 Å2
3----10.5161 Å2
Refine analyzeLuzzati coordinate error obs: 0.328 Å
Refinement stepCycle: LAST / Resolution: 2.54→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 47 54 3837
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013895HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.215289HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1365SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes554HARMONIC5
X-RAY DIFFRACTIONt_it3895HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion22.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion491SEMIHARMONIC5
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_contact4532SEMIHARMONIC4
LS refinement shellResolution: 2.54→2.68 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2786 155 5.61 %
Rwork0.2198 2606 -
all0.2231 2761 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59640.2032-0.08961.8322-0.01471.2061-0.007-0.11680.23430.20410.059-0.0226-0.18080.0652-0.052-0.28650.0349-0.0717-0.3444-0.0193-0.1544-17.134230.91851.5129
21.4185-0.7728-0.02261.64970.23781.4427-0.1372-0.1507-0.20170.39040.1151-0.05320.13810.05750.0221-0.18970.0507-0.0423-0.27720.0173-0.1197-19.782717.13977.3827
31.8033-0.6046-0.43191.7025-0.2950.63490.01480.1674-0.0845-0.29090.01830.00390.00380.0622-0.0331-0.262-0.00050.0007-0.3374-0.0302-0.1861-12.18566.2205-15.2052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 6-220
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 221-351
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 352-484

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