[English] 日本語
Yorodumi
- PDB-5lir: Structure of the SALTY Sigma cross-reacting protein 27A (SCRP-27A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lir
TitleStructure of the SALTY Sigma cross-reacting protein 27A (SCRP-27A) from Salmonella typhimurium
ComponentsSigma cross-reacting protein 27A (SCRP-27A)
KeywordsTRANSFERASE / Rossmann fold Class I glutamine amidotransferase-like
Function / homology
Function and homology information


Glyoxalase ElbB / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glyoxalase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchneider, S. / Mandel, M. / Sieber, S.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Natural-Product-Inspired Aminoepoxybenzoquinones Kill Members of the Gram-Negative Pathogen Salmonella by Attenuating Cellular Stress Response.
Authors: Mandl, F.A. / Kirsch, V.C. / Ugur, I. / Kunold, E. / Vomacka, J. / Fetzer, C. / Schneider, S. / Richter, K. / Fuchs, T.M. / Antes, I. / Sieber, S.A.
History
DepositionJul 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sigma cross-reacting protein 27A (SCRP-27A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9453
Polymers25,7321
Non-polymers2122
Water1,56787
1
A: Sigma cross-reacting protein 27A (SCRP-27A)
hetero molecules

A: Sigma cross-reacting protein 27A (SCRP-27A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8896
Polymers51,4652
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area3980 Å2
ΔGint-4 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.662, 99.662, 52.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Sigma cross-reacting protein 27A (SCRP-27A)


Mass: 25732.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: yhbL, STM3327 / Plasmid: pET300 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZLR6
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate pH 4.6 40 % PEG 200

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.75→44.86 Å / Num. obs: 30563 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.65
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 0.98 / CC1/2: 0.461 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHQ

1vhq


Resolution: 1.75→44.86 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 5.199 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18666 1409 4.6 %RANDOM
Rwork0.16603 ---
obs0.16702 29153 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.24 Å2-0 Å2
2---0.47 Å20 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Resolution: 1.75→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 14 87 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191705
X-RAY DIFFRACTIONr_bond_other_d0.0020.021685
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.9892323
X-RAY DIFFRACTIONr_angle_other_deg1.53433898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.33525.52267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.525158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211947
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02341
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1681.69894
X-RAY DIFFRACTIONr_mcbond_other1.1671.687893
X-RAY DIFFRACTIONr_mcangle_it1.652.5241121
X-RAY DIFFRACTIONr_mcangle_other1.6492.5261122
X-RAY DIFFRACTIONr_scbond_it2.2081.991811
X-RAY DIFFRACTIONr_scbond_other2.1971.991811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3022.8651196
X-RAY DIFFRACTIONr_long_range_B_refined5.60914.2181822
X-RAY DIFFRACTIONr_long_range_B_other5.6114.2371823
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 112 -
Rwork0.376 2104 -
obs--99.06 %
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)
15.80082.63013.86154.77162.57355.99280.1024-0.0343-0.24080.22780.0279-0.076-0.06090.2632-0.13040.0311-0.00380.02950.03440.02220.1438-12.056996.323766.5376
24.17230.25461.0852.69380.82661.9340.06650.0454-0.0517-0.0227-0.02380.3052-0.002-0.1553-0.04270.00360.00510.01160.0220.02770.141-18.388392.139561.6874
33.86692.8795-0.35684.7731-1.08640.29980.1987-0.31590.20490.7627-0.11670.4033-0.1985-0.0325-0.0820.1643-0.00840.10570.0795-0.04060.2011-18.450696.181472.3292
45.5435-1.13733.56712.2134-1.75955.2107-0.05840.11140.2868-0.17410.02940.3728-0.2338-0.38260.0290.05740.0463-0.03140.08030.00390.2424-20.3224104.594657.4168
50.8993-0.0152-0.45761.98191.00373.2025-0.00410.10940.15440.01410.01040.2453-0.2477-0.1497-0.00630.06060.0211-0.02020.02240.01590.173-11.8286109.836761.7745
65.5737-1.71710.03996.4853.984310.5909-0.04770.57040.5152-0.2676-0.00680.2805-0.0093-0.32220.05450.18590.0066-0.05030.12410.0660.2238-12.6754112.513847.9172
71.5620.1950.04625.03260.23692.6417-0.0970.1495-0.0038-0.2790.1307-0.1598-0.07940.1691-0.03360.0221-0.01980.00440.02820.00680.095-3.3824100.792254.7024
88.09070.10940.44487.59842.39129.6007-0.0352-0.40790.02720.50930.0743-0.2721-0.15770.5002-0.03910.06830.0031-0.00610.05790.00740.09961.3457102.531366.929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 20
2X-RAY DIFFRACTION2A21 - 64
3X-RAY DIFFRACTION3A65 - 91
4X-RAY DIFFRACTION4A92 - 115
5X-RAY DIFFRACTION5A116 - 159
6X-RAY DIFFRACTION6A160 - 172
7X-RAY DIFFRACTION7A173 - 211
8X-RAY DIFFRACTION8A212 - 220

+
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