[English] 日本語
Yorodumi
- PDB-4h5y: High-resolution crystal structure of Legionella pneumophila LidA ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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)

+
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://pdbjlvh1.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