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- PDB-4h5y: High-resolution crystal structure of Legionella pneumophila LidA ... -

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Basic information

Entry
Database: PDB / ID: 4h5y
TitleHigh-resolution crystal structure of Legionella pneumophila LidA (60-594)
ComponentsLidA protein, substrate of the Dot/Icm system
KeywordsPROTEIN TRANSPORT / twisted beta-hairpin repeat / coiled-coil / type IV secretion system / Rab-binding / Rab1 / Rab6 / Rab8 / PtdIns(3)P / PtdIns(4)P / membrane
Function / homologyHelix Hairpins - #2010 / Helix Hairpins / Helix non-globular / Special / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAn, X. / Ye, S. / Liu, Y. / Zheng, X. / Zhang, R.
CitationJournal: Protein Cell / Year: 2013
Title: The crystal structure of LidA, a translocated substrate of the Legionella pneumophila type IV secretion system.
Authors: Meng, G. / An, X. / Ye, S. / Liu, Y. / Zhu, W. / Zhang, R. / Zheng, X.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LidA protein, substrate of the Dot/Icm system


Theoretical massNumber of molelcules
Total (without water)65,4761
Polymers65,4761
Non-polymers00
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.554, 64.468, 164.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LidA protein, substrate of the Dot/Icm system


Mass: 65476.102 Da / Num. of mol.: 1 / Fragment: UNP residues 60-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lidA, LPC_2349 / Production host: Escherichia coli (E. coli) / References: UniProt: A5IFX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200 mM trimethylamine N-oxide, pH 8.0, 20% w/v PEG2000 MME, 1% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.1→82.187 Å / Num. all: 35335 / Num. obs: 35304 / % possible obs: 99.91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.15 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.026 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1754 4.97 %RANDOM
Rwork0.2008 ---
all0.2035 35335 --
obs0.2033 35304 99.91 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.312 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0091 Å2-0 Å20 Å2
2---7.1703 Å20 Å2
3---6.1612 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 0 422 4707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044347
X-RAY DIFFRACTIONf_angle_d0.7735808
X-RAY DIFFRACTIONf_dihedral_angle_d18.3071719
X-RAY DIFFRACTIONf_chiral_restr0.057628
X-RAY DIFFRACTIONf_plane_restr0.002751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15680.27261190.22472536X-RAY DIFFRACTION100
2.1568-2.22030.26441180.23192578X-RAY DIFFRACTION100
2.2203-2.29190.28081460.2242523X-RAY DIFFRACTION100
2.2919-2.37380.31551260.21442544X-RAY DIFFRACTION100
2.3738-2.46890.25611270.22112543X-RAY DIFFRACTION100
2.4689-2.58120.29091530.21312545X-RAY DIFFRACTION100
2.5812-2.71730.28111310.22412548X-RAY DIFFRACTION100
2.7173-2.88750.25931270.21912576X-RAY DIFFRACTION100
2.8875-3.11040.28251490.2232556X-RAY DIFFRACTION100
3.1104-3.42330.26641400.2012602X-RAY DIFFRACTION100
3.4233-3.91850.21831320.1772595X-RAY DIFFRACTION100
3.9185-4.9360.19921350.16532647X-RAY DIFFRACTION100
4.936-46.03660.2321510.19932757X-RAY DIFFRACTION100
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)
17.78580.53760.93122.71042.04714.5462-0.1671-0.74180.26550.92710.02640.1199-0.68460.04940.07970.40040.0498-0.01080.2284-0.0430.222849.315714.616162.9148
25.5289-1.71090.94841.7876-0.61032.1125-0.12030.25660.7935-0.07450.12040.00220.3086-0.1134-0.03050.2367-0.0164-0.03910.29330.0840.33965.32127.84657.4494
35.441-3.03571.38622.7923-1.02332.18070.1461-0.3237-0.18540.3065-0.1029-0.22540.12790.1754-0.02470.2902-0.0518-0.0450.20320.07440.309258.2854-2.184363.0844
44.7092-5.80813.94817.129-5.113.509-0.07780.03240.06870.0593-0.0176-0.34060.02550.1058-0.02130.21440.02570.04320.25680.03330.161846.879813.761744.3946
50.13320.11970.31061.93220.95641.3316-0.1231-0.10630.11030.13630.2071-0.04280.220.1647-0.02260.2609-0.0136-0.12650.1752-0.01770.394441.537365.712123.6225
68.5546-5.3477-8.02784.77675.61798.6619-0.01930.4116-0.6154-0.3807-0.35050.2769-0.3147-0.22270.28890.2046-0.0393-0.07730.167-0.05160.323340.902569.314916.0369
71.8772-1.59620.48352.8191-0.97981.0185-0.0614-0.10410.11260.01320.0215-0.19840.0921-0.07650.01370.1869-0.0377-0.06040.1604-0.06070.247228.273365.739125.4699
84.2996-0.0479-0.86183.63931.43914.7295-0.1316-0.038-0.2325-0.3836-0.03220.2894-0.1398-0.0310.19840.15690.0149-0.01490.1507-0.01230.13825.84645.573811.0745
93.003-1.6806-3.50982.26453.21494.8459-0.0856-0.12320.02410.04340.1491-0.2250.00150.4637-0.06560.24140.05250.04270.27510.01010.158639.935936.22810.6704
101.6376-2.69852.02617.6576-5.1594.00620.16880.0143-0.2752-0.1491-0.03850.1740.27090.2095-0.19880.23630.019-0.04130.1846-0.04090.204540.193611.582743.1109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 60:87)
2X-RAY DIFFRACTION2chain 'A' and (resseq 88:129)
3X-RAY DIFFRACTION3chain 'A' and (resseq 130:191)
4X-RAY DIFFRACTION4chain 'A' and (resseq 192:246)
5X-RAY DIFFRACTION5chain 'A' and (resseq 247:289)
6X-RAY DIFFRACTION6chain 'A' and (resseq 290:318)
7X-RAY DIFFRACTION7chain 'A' and (resseq 319:448)
8X-RAY DIFFRACTION8chain 'A' and (resseq 449:489)
9X-RAY DIFFRACTION9chain 'A' and (resseq 490:537)
10X-RAY DIFFRACTION10chain 'A' and (resseq 538:594)

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