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- PDB-7xp0: Crystal structure of PmiR from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7xp0
TitleCrystal structure of PmiR from Pseudomonas aeruginosa
ComponentsProbable transcriptional regulator
KeywordsSIGNALING PROTEIN / PmiR / 2-methylcitrate cycle / bacterial virulence
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsZhang, Y.X. / Liang, H.H. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2022
Title: PmiR senses 2-methylisocitrate levels to regulate bacterial virulence in Pseudomonas aeruginosa.
Authors: Cui, G. / Zhang, Y. / Xu, X. / Liu, Y. / Li, Z. / Wu, M. / Liu, J. / Gan, J. / Liang, H.
History
DepositionMay 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3815
Polymers25,0271
Non-polymers3544
Water362
1
A: Probable transcriptional regulator
hetero molecules

A: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,76210
Polymers50,0552
Non-polymers7078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-x-1,-y-1,z1
Buried area4150 Å2
ΔGint-171 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.352, 74.352, 188.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Probable transcriptional regulator / PmiR


Mass: 25027.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I5E1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 54 % / Description: block
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: MES/Sodium hydroxide, Magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 8283 / % possible obs: 98.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 35.53 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.037 / Rrim(I) all: 0.121 / Χ2: 0.941 / Net I/σ(I): 15.1 / Num. measured all: 71992
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.694.60.4347500.660.1970.4820.96791.7
2.69-2.85.70.4087930.8240.1740.4460.90197.1
2.8-2.936.80.3348180.930.1330.3610.93599.6
2.93-3.087.20.278160.9680.1050.2910.91799.4
3.08-3.2880.2098150.9830.0740.2220.89699.5
3.28-3.539.50.1648270.9910.0530.1730.89299.8
3.53-3.8810.60.1258330.9920.0380.1310.94999.8
3.88-4.4410.90.1138440.9890.0340.1180.95899.6
4.44-5.5911.90.1178600.9930.0340.1221.09399.8
5.59-3010.70.1029270.9910.0330.1070.85399.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model generated by Alphafold2

Resolution: 2.61→29.38 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 353 4.92 %
Rwork0.1996 6816 -
obs0.2022 7169 84.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.47 Å2 / Biso mean: 49.669 Å2 / Biso min: 13.8 Å2
Refinement stepCycle: final / Resolution: 2.61→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 16 2 1619
Biso mean--72.29 46.27 -
Num. residues----200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.61-2.980.3166720.24281455152756
2.99-3.760.27671410.2182590273198
3.76-29.380.221400.179627712911100
Refinement TLS params.Method: refined / Origin x: -32.8019 Å / Origin y: -26.1226 Å / Origin z: -23.2835 Å
111213212223313233
T0.1874 Å2-0.028 Å20.0802 Å2-0.3578 Å20.0632 Å2--0.2114 Å2
L2.2696 °20.092 °20.2337 °2-1.8619 °20.1463 °2--2.7702 °2
S0.0333 Å °0.5642 Å °0.3555 Å °-0.2477 Å °0.0605 Å °0.116 Å °-0.4655 Å °0.2118 Å °-0.0648 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 226
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1 - 3
4X-RAY DIFFRACTION1allD1 - 2

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