[English] 日本語
Yorodumi
- PDB-4ber: Crystal structure of the Legionella pneumophila FIC domain-contai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ber
TitleCrystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein in complex with cytidine monophosphate
ComponentsPHOSPHOCHOLINE TRANSFERASE ANKX
KeywordsTRANSFERASE / 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 / PHOSPHATE ION / Phosphocholine transferase AnkX
Similarity search - Component
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,8989
Polymers109,7792
Non-polymers1,1187
Water1,31573
1
A: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4955
Polymers54,8901
Non-polymers6054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOCHOLINE TRANSFERASE ANKX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4034
Polymers54,8901
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.330, 103.560, 224.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

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


Mass: 54889.660 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 / 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.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growpH: 8.5 / Details: 15% PEG 20000, 0.1 M TRIS PH 8.5

-
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: 2.6→46.28 Å / Num. obs: 42690 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 62.69 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.16
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BEP

4bep


Resolution: 2.6→46.28 Å / Cor.coef. Fo:Fc: 0.9145 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.434 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.424 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.264
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 2135 5 %RANDOM
Rwork0.2056 ---
obs0.2072 42690 99.8 %-
Displacement parametersBiso mean: 66.29 Å2
Baniso -1Baniso -2Baniso -3
1--16.6577 Å20 Å20 Å2
2--15.291 Å20 Å2
3---1.3667 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7578 0 68 73 7719
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017850HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1810633HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2772SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes216HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1120HARMONIC5
X-RAY DIFFRACTIONt_it7850HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion22.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion992SEMIHARMONIC5
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_contact8968SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2704 155 5.01 %
Rwork0.2397 2941 -
all0.2413 3096 -
obs--99.8 %
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)
12.0649-0.4997-0.00123.13360.55032.1735-0.0711-0.3395-0.02750.31420.1311-0.73380.00940.4401-0.0599-0.2390.0352-0.0635-0.1365-0.00040.004725.046450.184935.3732
21.7586-0.81680.19833.58111.0422.3441-0.0401-0.2379-0.29030.2892-0.04880.05410.0815-0.14530.089-0.11030.01430.0229-0.06210.0186-0.044810.891647.414835.8588
30.28020.4988-0.74986.2182.46342.06870.08950.26480.0917-0.5883-0.14130.0796-0.135-0.21390.0519-0.05170.046-0.0287-0.1268-0.0537-0.112910.591233.196712.6934
41.5216-0.70470.04563.2972-0.32941.4132-0.1091-0.1485-0.16820.39230.12530.6607-0.1714-0.342-0.0162-0.01380.08480.0892-0.15150.0324-0.1632-10.866289.00625.0206
50.8648-0.4028-0.2523.3761-0.5211.8133-0.0863-0.36010.06350.8910.0127-0.1077-0.34160.11060.07360.30040.07580.0235-0.09550.0067-0.25770.791192.221333.7162
60.76371.35540.7175.7027-0.23231.27680.0403-0.0622-0.07230.097-0.0145-0.36090.17590.1173-0.0259-0.02540.03170.0071-0.1229-0.0122-0.164112.2172107.39213.625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - 220 }
2X-RAY DIFFRACTION2{ A|221 - 351 }
3X-RAY DIFFRACTION3{ A|352 - 477 }
4X-RAY DIFFRACTION4{ B|1 - 220 }
5X-RAY DIFFRACTION5{ B|221 - 351 }
6X-RAY DIFFRACTION6{ B|352 - 479 }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more