[English] 日本語
Yorodumi
- PDB-5suj: Crystal structure of uncharacterized protein LPG2148 from Legione... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5suj
TitleCrystal structure of uncharacterized protein LPG2148 from Legionella pneumophila
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homologyUncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.356 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: Cell Rep / Year: 2018
Title: Discovery of Ubiquitin Deamidases in the Pathogenic Arsenal of Legionella pneumophila.
Authors: Valleau, D. / Quaile, A.T. / Cui, H. / Xu, X. / Evdokimova, E. / Chang, C. / Cuff, M.E. / Urbanus, M.L. / Houliston, S. / Arrowsmith, C.H. / Ensminger, A.W. / Savchenko, A.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)92,7002
Polymers92,7002
Non-polymers00
Water4,432246
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)46,3501
Polymers46,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)46,3501
Polymers46,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.884, 135.889, 64.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Uncharacterized protein


Mass: 46349.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2148
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5ZTL3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium formate, 20% PEG3350, 4% Sucrose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 44965 / % possible obs: 99.7 % / Redundancy: 8.1 % / Biso Wilson estimate: 28.88 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.03 / Rrim(I) all: 0.087 / Χ2: 0.897 / Net I/av σ(I): 26.737 / Net I/σ(I): 8.5 / Num. measured all: 363605
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.395.50.77821770.8360.3360.8520.91197.4
2.39-2.436.30.80821760.850.3310.8760.90999.2
2.43-2.487.50.72922120.9220.2760.7810.90299.5
2.48-2.5380.67522090.9450.2470.720.91999.6
2.53-2.598.30.60122140.9550.2170.640.92799.8
2.59-2.658.40.53222490.9570.1910.5660.90699.8
2.65-2.718.40.45521950.9740.1630.4840.92599.7
2.71-2.798.40.36522430.9770.1310.3880.90899.9
2.79-2.878.50.2822000.9840.10.2980.92599.9
2.87-2.968.40.21222370.9910.0760.2250.917100
2.96-3.078.50.16222430.9940.0580.1720.89299.9
3.07-3.198.60.12122410.9960.0430.1290.886100
3.19-3.338.60.09222500.9970.0330.0980.861100
3.33-3.518.60.06722510.9980.0240.0710.841100
3.51-3.738.50.05422650.9980.0190.0570.804100
3.73-4.028.50.04722450.9980.0170.050.793100
4.02-4.428.50.04622840.9980.0170.0490.936100
4.42-5.068.40.05122930.9980.0190.0551.218100
5.06-6.378.10.04723240.9970.0170.050.969100
6.37-507.80.02624570.9990.010.0280.60899.8

-
Processing

Software
NameVersionClassification
PHENIXdev_2386refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.356→43.573 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2225 3651 5.05 %
Rwork0.1787 --
obs0.1809 42078 84.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.62 Å2 / Biso mean: 40.2227 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 2.356→43.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 0 246 6310
Biso mean---36.27 -
Num. residues----757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086206
X-RAY DIFFRACTIONf_angle_d0.9128366
X-RAY DIFFRACTIONf_chiral_restr0.049909
X-RAY DIFFRACTIONf_plane_restr0.0061091
X-RAY DIFFRACTIONf_dihedral_angle_d11.7083802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3558-2.38680.302570.23693699330
2.3868-2.41950.3052610.2271223128439
2.4195-2.45410.2379730.23651394146744
2.4541-2.49070.2763930.22671649174254
2.4907-2.52960.28900.22911887197760
2.5296-2.57110.24331170.22382074219166
2.5711-2.61540.31431160.23172255237172
2.6154-2.6630.27781220.21692406252877
2.663-2.71420.27521320.22482537266982
2.7142-2.76960.29541490.21992747289687
2.7696-2.82980.26161500.23012845299592
2.8298-2.89560.28021770.22132979315696
2.8956-2.9680.29451430.21593072321599
2.968-3.04830.23471570.22063124328199
3.0483-3.13790.24241780.214431083286100
3.1379-3.23920.25031830.208531413324100
3.2392-3.35490.24771590.185131233282100
3.3549-3.48920.25191690.173531113280100
3.4892-3.64790.20041880.159731153303100
3.6479-3.84010.19651500.149631553305100
3.8401-4.08060.20681860.136930843270100
4.0806-4.39530.15581640.125831443308100
4.3953-4.83720.17561410.119931483289100
4.8372-5.53590.16431630.142431493312100
5.5359-6.970.2031770.197831073284100
6.97-43.58090.20131560.18523107326399
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)
12.6776-0.1248-0.2261.01660.17361.7411-0.13870.287-0.3481-0.11190.1807-0.02070.2513-0.0119-0.04840.2059-0.06330.00920.1478-0.07430.272111.8871-20.498643.2292
21.6486-1.40060.82922.3236-1.21550.76330.0856-0.2253-0.29060.08670.0395-0.16770.09630.0455-0.07040.24-0.0155-0.04470.34370.02860.2517117.3891-34.328666.3203
30.6446-0.69710.45291.2892-0.19020.28780.0041-0.7083-0.39430.38210.18620.0677-0.0930.08430.07770.22780.0579-0.0860.520.30640.3845115.6729-39.273472.7205
43.65240.44390.27941.2827-0.48551.5289-0.1034-0.46210.07330.10490.06080.051-0.0309-0.28740.01640.1694-0.01060.03520.1302-0.05610.0953106.0738-16.588557.1947
52.79070.0466-0.03451.58760.05241.8691-0.0572-0.017-0.0665-0.07560.15460.34140.0081-0.265-0.10030.1663-0.015-0.02260.19010.01240.310878.4386-18.001942.437
60.44311.44060.27544.4971.3273-0.22830.0046-0.1114-0.12530.13710.029-0.4126-0.07270.1894-0.05480.24950.0166-0.09310.2967-0.09070.297874.5143-47.31128.4108
73.29790.12580.46821.41020.30972.0124-0.10430.22050.0501-0.21150.14620.1587-0.17050.0073-0.03880.1546-0.0405-0.01430.12390.02910.125585.9013-17.467338.174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 77 )A13 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 217 )A78 - 217
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 250 )A218 - 250
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 395 )A251 - 395
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 131 )B13 - 131
6X-RAY DIFFRACTION6chain 'B' and (resid 132 through 250 )B132 - 250
7X-RAY DIFFRACTION7chain 'B' and (resid 251 through 395 )B251 - 395

+
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