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

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Basic information

Entry
Database: PDB / ID: 4bep
TitleCrystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein (apo-form)
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
Phosphocholine transferase AnkX
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.14 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: Data collection / Database references / Other
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1416
Polymers117,8292
Non-polymers3124
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-82.9 kcal/mol
Surface area41550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.268, 91.633, 239.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 5 - 477 / Label seq-ID: 33 - 505

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.214, 0.9482, -0.2348), (0.9573, 0.1557, -0.2436), (-0.1944, -0.2769, -0.941)
Vector: -11.3057, 19.3125, 48.2073)

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Components

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


Mass: 58914.266 Da / Num. of mol.: 2 / Fragment: FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA 1 / Plasmid: PDEST17 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsL247P (CLONING ARTEFACT) N-TERMINAL HIS-6 TAG NOT CLEAVED BY TEV PROTEASE

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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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growpH: 8
Details: 0.2 M POTASSIUM THIOCYANATE, 15-25% PEG 3350, 0.05 M HEPES PH 7.8-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.14→44 Å / Num. obs: 20682 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.33
Reflection shellResolution: 3.14→3.33 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.59 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.14→44 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.879 / SU B: 53.847 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28557 1118 5.1 %RANDOM
Rwork0.22789 ---
obs0.2308 20681 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.032 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å20 Å2
2--2.39 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 3.14→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7509 0 16 6 7531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197693
X-RAY DIFFRACTIONr_bond_other_d0.0060.027341
X-RAY DIFFRACTIONr_angle_refined_deg1.651.98310398
X-RAY DIFFRACTIONr_angle_other_deg1.313316979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9515939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44825.083362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.299151315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.081530
X-RAY DIFFRACTIONr_chiral_restr0.090.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218665
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021713
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27183 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.139→3.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 87 -
Rwork0.27 1427 -
obs--94.92 %
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)
11.5454-0.13130.28251.33940.16412.5377-0.01160.12280.5029-0.21370.0997-0.2595-0.2770.0777-0.08820.45740.00660.0040.0231-0.00670.5721-26.465-2.80740.4041
20.97560.45231.4832.19431.08742.37830.1142-0.24080.1636-0.1126-0.2271-0.43940.1284-0.19520.11290.13940.0836-0.01571.0827-0.26370.2504-8.3155-5.310353.7693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 482
2X-RAY DIFFRACTION2B5 - 477

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