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

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Basic information

Entry
Database: PDB / ID: 4bet
TitleCrystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein (inactive H229A mutant) in complex with cytidine-diphosphate-choline
ComponentsPHOSPHOCHOLINE TRANSFERASE ANKX
KeywordsTRANSFERASE / PHOSPHOCHOLINATION / TYPE IV SECRETION SYSTEM EFFECTOR / CYTIDINE- DIPHOSPHATE-CHOLINE
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
Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...Fido-like domain superfamily / Fido domain / Fic/DOC family / 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
Chem-CDC / Phosphocholine transferase AnkX
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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

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Assembly

Deposited unit
A: PHOSPHOCHOLINE TRANSFERASE ANKX
B: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,20611
Polymers116,5692
Non-polymers1,6379
Water2,054114
1
A: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules

B: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,20611
Polymers116,5692
Non-polymers1,6379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area5530 Å2
ΔGint-107.2 kcal/mol
Surface area40550 Å2
MethodPISA
2
B: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules

A: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,20611
Polymers116,5692
Non-polymers1,6379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area5530 Å2
ΔGint-107.2 kcal/mol
Surface area40550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.100, 122.150, 75.700
Angle α, β, γ (deg.)90.00, 107.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.470724, 0.003868, 0.882272), (-0.004307, -0.999989, 0.002086), (0.88227, -0.002818, 0.470735)
Vector: 21.939, -62.005, 36.011)

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Components

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


Mass: 58284.461 Da / Num. of mol.: 2 / Fragment: FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: INACTIVE MUTANT / Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA 1 / 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-CDC / [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM / Citicoline


Mass: 488.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26N4O11P2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.5 Å3/Da / Density % sol: 50.9 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M LITHIUM SULFATE, 14% PEG 4000, 0.1 M TRIS PH 7.5

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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: May 2, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.55→43.89 Å / Num. obs: 36935 / % possible obs: 98.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 60.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.02
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.75 / % possible all: 97.4

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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: 2.55→43.89 Å / Cor.coef. Fo:Fc: 0.9232 / Cor.coef. Fo:Fc free: 0.8891 / SU R Cruickshank DPI: 0.637 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.545 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.291
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1847 5 %RANDOM
Rwork0.2033 ---
obs0.2055 36935 98.7 %-
Displacement parametersBiso mean: 69.76 Å2
Baniso -1Baniso -2Baniso -3
1--15.1829 Å20 Å212.6711 Å2
2--18.4664 Å20 Å2
3----3.2834 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.55→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 100 114 7853
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017982HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2210851HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2820SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes220HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1129HARMONIC5
X-RAY DIFFRACTIONt_it7982HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion22.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1003SEMIHARMONIC5
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_contact9177SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2713 142 4.99 %
Rwork0.256 2704 -
all0.2568 2846 -
obs--98.7 %
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)
11.2581-0.16280.28622.78510.11121.87130.0908-0.0389-0.29640.24650.07070.19080.2773-0.1012-0.1615-0.06190.0008-0.2692-0.24420.06080.061717.4425-31.269333.2657
21.9853-0.22530.65952.2811-0.79521.3537-0.0177-0.15820.08530.47730.15290.321-0.2758-0.2293-0.13520.04380.0733-0.1769-0.16250.04980.018314.6598-17.307539.0132
3-0.1307-0.94870.39292.1036-1.32863.1498-0.01940.1196-0.00190.0573-0.1045-0.6250.08620.35220.1239-0.152-0.0273-0.1751-0.1407-0.02290.111930.5057-6.628720.8438
41.36410.04770.62792.812-0.13991.8903-0.08290.15370.1396-0.00780.0066-0.3178-0.37650.11110.0763-0.0574-0.0469-0.1489-0.2241-0.0164-0.043742.9507-30.729767.1494
51.38580.34870.27272.64430.57161.9431-0.03830.1672-0.2756-0.03410.1172-0.6429-0.02730.277-0.079-0.1404-0.0219-0.1335-0.1416-0.05640.07449.3507-44.62267.316
61.45710.61861.4322.97261.13541.23640.1068-0.19980.04320.4152-0.09820.36920.0793-0.2124-0.0086-0.07420.0145-0.0647-0.11930.0245-0.009825.9824-55.449272.7413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|5 - 220 }
2X-RAY DIFFRACTION2{ A|221 - 351 }
3X-RAY DIFFRACTION3{ A|352 - 484 }
4X-RAY DIFFRACTION4{ B|6 - 220 }
5X-RAY DIFFRACTION5{ B|221 - 351 }
6X-RAY DIFFRACTION6{ B|352 - 484 }

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