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- PDB-5lir: Structure of the SALTY Sigma cross-reacting protein 27A (SCRP-27A... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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