[English] 日本語
Yorodumi
- PDB-4hfv: Crystal structure of lpg1851 protein from Legionella pneumophila ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hfv
TitleCrystal structure of lpg1851 protein from Legionella pneumophila (putative T4SS effector)
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / effector
Function / homology
Function and homology information


de novo design (two linked rop proteins) - #330 / Substrate of the Dot/Icm secretion system / Putative substrate of the Dot/Icm secretion system / Putative substrate of the Dot/Icm secretion system superfamily / Substrate of the Dot/Icm secretion system, putative / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / de novo design (two linked rop proteins) / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / SUCCINIC ACID / Dot/Icm T4SS effector
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.901 Å
AuthorsMichalska, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Mol Syst Biol / Year: 2016
Title: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila.
Authors: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. ...Authors: Urbanus, M.L. / Quaile, A.T. / Stogios, P.J. / Morar, M. / Rao, C. / Di Leo, R. / Evdokimova, E. / Lam, M. / Oatway, C. / Cuff, M.E. / Osipiuk, J. / Michalska, K. / Nocek, B.P. / Taipale, M. / Savchenko, A. / Ensminger, A.W.
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5233
Polymers22,2131
Non-polymers3102
Water3,549197
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0466
Polymers44,4262
Non-polymers6204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3450 Å2
ΔGint-4 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.339, 43.339, 205.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Components

#1: Protein Uncharacterized protein


Mass: 22213.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg1851 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5ZUE7
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M diammonium citrate, 20% PEG3350, 1/70 thermolysin, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794534 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794534 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 18726 / Num. obs: 18684 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.06 / Num. unique all: 899 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
autoSHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.901→27.723 Å / SU ML: 0.2 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.19 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT RIDING POSITIONS, THE PROTEIN WAS SUBJECTED TO IN SITU PROTEOLYSIS, THEREFORE THE EXACT LENGTH OF THE CRYSTALLIZED POLYPEPTIDE COULD NOT BE DETERMINED
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 951 5.11 %random
Rwork0.1829 ---
all0.1854 18596 --
obs0.1854 18596 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→27.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 21 197 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151663
X-RAY DIFFRACTIONf_angle_d1.362250
X-RAY DIFFRACTIONf_dihedral_angle_d17.48655
X-RAY DIFFRACTIONf_chiral_restr0.08248
X-RAY DIFFRACTIONf_plane_restr0.007293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-2.00120.28391470.25032429X-RAY DIFFRACTION100
2.0012-2.12660.26421550.20762452X-RAY DIFFRACTION100
2.1266-2.29070.27571350.20992491X-RAY DIFFRACTION100
2.2907-2.52110.22741320.17522484X-RAY DIFFRACTION100
2.5211-2.88560.24211270.1742537X-RAY DIFFRACTION100
2.8856-3.63420.22211250.18272542X-RAY DIFFRACTION100
3.6342-27.72550.20761300.16532710X-RAY DIFFRACTION99
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)
14.8141-2.23711.58712.88242.01187.714-0.6403-0.00541.1762-0.39380.4457-0.0273-1.25260.6530.13220.32670.0237-0.03620.2598-0.01650.2979-4.31855.561212.763
21.0824-0.8111-0.33631.04280.47170.9291-0.07950.1493-0.6202-0.3779-0.1150.51640.1032-0.19820.01520.1327-0.01710.00360.1022-0.0420.1357-1.6961-13.03324.1502
33.0823-2.74650.07723.88910.79375.6533-0.18770.0253-1.13450.3494-0.21470.6310.9396-0.72890.55670.2894-0.0270.08440.1488-0.14310.31360.2968-24.2239-2.3877
42.7655-0.86782.83451.863-0.44046.78320.1876-0.1791-0.79250.0856-0.03410.40950.6965-0.96350.4940.5-0.03310.0850.2154-0.0510.2884-1.0564-23.06246.9704
51.08230.4882-0.38331.9964-0.2712.694-0.110.1766-0.16080.0098-0.02740.22941.1714-0.4658-0.0296-0.0648-0.04840.03660.1980.01880.1188-3.7894-14.514915.7876
60.96910.87050.81551.65870.22051.5356-0.01670.1310.0816-0.06040.0035-0.0072-0.1405-0.1252-0.00360.0939-0.0006-0.00270.10230.00480.07925.0029-4.353411.7816
77.9361-1.621.83430.52120.10251.86910.18610.9260.87980.0861-0.5422-0.0255-1.64070.242-0.40660.4508-0.00420.02550.1468-0.02390.11420.74676.90410.036
80.5944-0.2193-0.41910.7269-0.30283.50140.167-0.04520.18070.0624-0.30810.5326-0.684-0.0529-0.17660.16360.00120.00030.181-0.03530.1069-2.4238-2.097924.3625
91.4171-0.58640.42090.8752-0.23410.5545-0.0349-0.44910.05830.34020.06370.03620.5929-0.0068-0.01220.254-0.03920.04210.2241-0.02880.144-2.0031-18.280929.5647
102.405-0.6917-1.11854.63360.10192.13730.1050.11130.38980.35460.1067-0.8081-0.39930.02590.0050.1549-0.01150.00260.1776-0.00670.14015.2755.993529.3459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 : 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 : 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 : 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 : 45 )
5X-RAY DIFFRACTION5chain 'A' and (resid 46 : 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 : 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 : 118 )
8X-RAY DIFFRACTION8chain 'A' and (resid 119 : 136 )
9X-RAY DIFFRACTION9chain 'A' and (resid 137 : 159 )
10X-RAY DIFFRACTION10chain 'A' and (resid 160 : 189 )

+
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