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- PDB-8ylj: Crystal structure of Pectobacterium atrosepticum PecS in complex ... -

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Basic information

Entry
Database: PDB / ID: 8ylj
TitleCrystal structure of Pectobacterium atrosepticum PecS in complex with uric acid
ComponentsRegulatory protein
KeywordsTRANSCRIPTION / Transcription factor
Function / homologyMarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / URIC ACID / Regulatory protein
Function and homology information
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSong, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1I1A1A01068105 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of transcriptional regulation by UrtR in response to uric acid.
Authors: Song, W.S. / Ki, D.U. / Cho, H.Y. / Kwon, O.H. / Cho, H. / Yoon, S.I.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2332
Polymers19,0651
Non-polymers1681
Water66737
1
A: Regulatory protein
hetero molecules

A: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4664
Polymers38,1302
Non-polymers3362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7950 Å2
ΔGint-55 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.528, 78.796, 39.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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Components

#1: Protein Regulatory protein


Mass: 19064.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: pecS, ECA2036 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D5K4
#2: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Hepes, lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 10908 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.96 Å2 / CC1/2: 0.989 / Net I/σ(I): 25.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 529 / CC1/2: 0.675 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8YLF

8ylf


Resolution: 2.05→26.26 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2737 539 4.96 %
Rwork0.2267 10323 -
obs0.2289 10862 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.71 Å2
Refinement stepCycle: LAST / Resolution: 2.05→26.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 12 37 1284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171266
X-RAY DIFFRACTIONf_angle_d0.43091719
X-RAY DIFFRACTIONf_chiral_restr0.0326204
X-RAY DIFFRACTIONf_plane_restr0.0039222
X-RAY DIFFRACTIONf_dihedral_angle_d12.0509461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.260.28531160.26922534X-RAY DIFFRACTION99.62
2.26-2.580.30841540.25292516X-RAY DIFFRACTION100
2.58-3.250.28981460.24562563X-RAY DIFFRACTION100
3.25-26.260.24881230.2032710X-RAY DIFFRACTION99.47
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)
15.53863613554-0.2852804228740.5723317640722.7660211009-0.6912098486162.33348300295-0.02955443723840.115566478940.06882687660260.222811950856-0.02163610562010.0179571882801-0.0524346717801-0.229621804523-0.1072289431440.154701263290.05957563494920.03528681838020.2057021344880.0116468027910.162477102743-35.1745931892-2.56002328552-6.95645128876
22.21470157042-0.522287770260.1099142789282.87018573473-1.158149845542.41957630075-0.05099781876191.202886992930.513451373814-0.4669255796140.2368529363580.09926692137370.0573675936963-0.129151532405-0.06178700550940.330264094954-0.0821796767167-0.01844910498880.5908486800970.1993147284680.316433076756-8.526042955827.59939313303-20.8785870515
34.905265570742.54320644448-0.6468879983523.4346921173-0.9347905126222.022344238090.134109636398-0.2325806021941.018268380430.0839676145247-0.2561366560580.0691973749482-0.2705363036050.02441219455560.004697343688930.2846511562770.009112812030240.01046023821780.203479324320.02549742312310.384412178202-20.19563026289.31322615028-4.05416112865
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 60 )14 - 601 - 47
22chain 'A' and (resid 61 through 128 )61 - 12848 - 115
33chain 'A' and (resid 129 through 175 )129 - 175116 - 162

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