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- PDB-4akf: Crystal structure of VipD from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 4akf
TitleCrystal structure of VipD from Legionella pneumophila
ComponentsVIPD
KeywordsTRANSFERASE
Function / homology
Function and homology information


lipid catabolic process / hydrolase activity
Similarity search - Function
Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLEGIONELLA PNEUMOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsLee, K.-H. / Ku, B. / Oh, B.-H.
CitationJournal: Plos Pathog. / Year: 2012
Title: Vipd of Legionella Pneumophila Targets Activated Rab5 and Rab22 to Interfere with Endosomal Trafficking in Macrophages
Authors: Ku, B. / Lee, K.-H. / Park, W.S. / Yang, C.-S. / Ge, J. / Lee, S.-G. / Cha, S.-S. / Shaow, F. / Heo, D. / Jumg, J.U. / Oh, B.-H.
History
DepositionFeb 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VIPD


Theoretical massNumber of molelcules
Total (without water)64,3361
Polymers64,3361
Non-polymers00
Water1,54986
1
A: VIPD

A: VIPD


Theoretical massNumber of molelcules
Total (without water)128,6732
Polymers128,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation48_434-z-1/2,-y-3/2,-x-1/21
Buried area4600 Å2
ΔGint-30.1 kcal/mol
Surface area49260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.757, 252.757, 252.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

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Components

#1: Protein VIPD


Mass: 64336.418 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA-1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5ZRP9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.2 Å3/Da / Density % sol: 76.3 % / Description: NONE
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 100 MM TRIS-HCL (PH 8.0), 1.0 M AMMONIUM CITRATE TRIBASIC (PH 7.0) AND 10 MM MGCL2.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 34134 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.5
Reflection shellResolution: 2.8→2.85 Å / Mean I/σ(I) obs: 2.3 / % possible all: 98.9

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Processing

SoftwareName: CNS / Version: 1.2 / Classification: refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.2333 1504 4.9 %
Rwork0.2144 --
obs0.2144 30527 99.5 %
Solvent computationBsol: 27.0427 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 0 86 4466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0083
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3266
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.982.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4GOL_XPLOR_PAR

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