[English] 日本語
Yorodumi
- PDB-5es2: The crystal structure of a functionally uncharacterized protein L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5es2
TitleThe crystal structure of a functionally uncharacterized protein LPG0634 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
ComponentsUncharacterized protein LPG0634
KeywordsStructural Genomics / Unknown Function / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyPutative substrate of the Dot/Icm secretion system / Putative substrate of the Dot/Icm secretion system superfamily / Substrate of the Dot/Icm secretion system, putative / ACETATE ION / Type IV secretion protein Dot
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074942 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: The crystal structure of a functionally uncharacterized protein LPG0634 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Authors: Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein LPG0634
B: Uncharacterized protein LPG0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,22725
Polymers99,3412
Non-polymers1,88523
Water93752
1
A: Uncharacterized protein LPG0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,98917
Polymers49,6711
Non-polymers1,31816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein LPG0634
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2388
Polymers49,6711
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.070, 97.322, 100.447
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Uncharacterized protein LPG0634


Mass: 49670.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0634 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZXU7
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M LiSO4, 0.1M HEPES, 25% PEG335

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→36.5 Å / Num. all: 35558 / Num. obs: 35558 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 24.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3.06 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→36.202 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1800 5.19 %Random selection
Rwork0.191 ---
obs0.1942 34711 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→36.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 106 52 6138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016143
X-RAY DIFFRACTIONf_angle_d0.3428285
X-RAY DIFFRACTIONf_dihedral_angle_d9.9352252
X-RAY DIFFRACTIONf_chiral_restr0.015966
X-RAY DIFFRACTIONf_plane_restr0.0021057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.67030.34181430.27482526X-RAY DIFFRACTION100
2.6703-2.74890.361300.26132521X-RAY DIFFRACTION100
2.7489-2.83760.29161200.24982577X-RAY DIFFRACTION100
2.8376-2.93890.32651360.24282537X-RAY DIFFRACTION100
2.9389-3.05660.32871340.25562525X-RAY DIFFRACTION100
3.0566-3.19560.26961480.24792514X-RAY DIFFRACTION100
3.1956-3.3640.27741410.2282532X-RAY DIFFRACTION100
3.364-3.57450.26421320.21342542X-RAY DIFFRACTION100
3.5745-3.85030.22271600.17952516X-RAY DIFFRACTION100
3.8503-4.23720.20521230.15752575X-RAY DIFFRACTION100
4.2372-4.84910.20651530.15222513X-RAY DIFFRACTION100
4.8491-6.10460.24761630.17852532X-RAY DIFFRACTION100
6.1046-36.20580.25761170.1542501X-RAY DIFFRACTION95
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)
13.62541.3919-0.72254.27580.01121.7914-0.05740.1220.0721-0.1277-0.03030.1045-0.0768-0.01510.09050.26540.006-0.05170.37460.00860.368944.380928.9262131.6661
22.484-0.3749-0.21472.0134-0.66723.18130.09450.169-0.0095-0.12470.04080.17590.2474-0.3479-0.14030.2835-0.0232-0.0190.4257-0.05550.4816.643610.0312146.9667
35.2366-0.0589-1.63642.0449-0.29634.42320.09150.1370.263-0.04930.0788-0.0443-0.1492-0.2045-0.14440.3058-0.04950.00540.2713-0.02950.412926.061518.7277142.3565
41.69831.0877-0.87983.9878-1.29084.3971-0.0026-0.42320.19771.250.34970.3035-0.80460.1479-0.31241.24610.1848-0.02490.7694-0.25520.809727.450949.835296.8159
52.1869-0.3789-1.79336.7564-1.77674.56930.23050.3215-0.0708-0.10920.1143-0.037-0.6081-0.0021-0.25440.77860.078-0.04830.5376-0.1770.55931.324946.70988.3274
64.69541.7921-2.27089.0029-1.12445.62360.1131-0.35940.20310.72210.1308-0.8222-0.32350.8744-0.27620.68420.0836-0.14530.6469-0.30660.720138.004840.067389.9064
71.3506-1.9676-1.40963.64040.77022.7328-0.195-0.3734-0.08460.71790.11760.10570.04870.00190.06220.6655-0.005-0.07560.7478-0.22970.632933.488628.532491.0641
82.241-0.0723-0.41065.24482.47316.8649-0.1232-0.3197-0.27050.60740.0875-0.21850.13920.06990.03360.47280.15450.00360.49390.00560.406239.54033.293878.8095
95.73080.66853.91853.47960.00477.0323-0.2659-0.9892-0.10780.94090.3099-0.29870.03020.318-0.05390.59670.1877-0.05330.687-0.10450.437140.740510.637785.5307
104.90330.57452.62964.6012-0.26526.930.0169-0.99-0.17991.14320.19110.80340.1054-0.9099-0.11370.54920.11260.13850.5665-0.01690.489726.61679.561679.4858
115.38331.1356-1.43336.33410.54595.8206-0.0259-0.34310.37180.49350.4846-1.0971-0.56480.8604-0.47510.59120.1253-0.1490.7279-0.20650.574746.736220.136682.8418
124.8438-2.1462-3.11584.30511.9876.0956-0.2453-0.3130.25880.69690.06390.54270.319-0.59330.15130.6112-0.00220.0970.6759-0.13270.604223.966524.972188.2954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 317 )
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 398 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 62 )
5X-RAY DIFFRACTION5chain 'B' and (resid 63 through 107 )
6X-RAY DIFFRACTION6chain 'B' and (resid 108 through 136 )
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 202 )
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 254 )
9X-RAY DIFFRACTION9chain 'B' and (resid 255 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 289 through 317 )
11X-RAY DIFFRACTION11chain 'B' and (resid 318 through 365 )
12X-RAY DIFFRACTION12chain 'B' and (resid 366 through 400 )

+
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