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- PDB-7xp1: Crystal structure of PmiR from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7xp1
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
ALPHA-METHYLISOCITRIC ACID / Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Nov 29, 2023Group: 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)25,6797
Polymers25,0271
Non-polymers6526
Water1086
1
A: Probable transcriptional regulator
hetero molecules

A: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,35914
Polymers50,0552
Non-polymers1,30412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area5330 Å2
ΔGint-141 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.021, 74.021, 186.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 12 molecules

#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-MIC / ALPHA-METHYLISOCITRIC ACID


Mass: 206.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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 / pH: 5.8 / Details: MES/Sodium hydroxide, Magnesium sulfate / PH range: 5.6-6.0

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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: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 9006 / % possible obs: 96.4 % / Redundancy: 17.7 % / Biso Wilson estimate: 30.55 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.01 / Rrim(I) all: 0.048 / Χ2: 0.971 / Net I/σ(I): 11.4 / Num. measured all: 159703
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.598.10.3936460.9250.1270.4160.89271.6
2.59-2.699.80.4178420.8440.1280.4380.84692.5
2.69-2.8213.30.3979130.9430.1090.4120.83299.2
2.82-2.9615.40.299120.9860.0740.30.902100
2.96-3.1515.80.1979210.9970.0490.2030.967100
3.15-3.3919.50.1599230.9990.0360.1631.045100
3.39-3.7321.60.0789310.9990.0170.081.10799.9
3.73-4.2722.30.0519360.9990.0110.0521.13399.9
4.27-5.3824.80.03895310.0080.039199.9
5.38-3022.30.03102910.0070.0310.78899.6

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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: 7XP0

7xp0


Resolution: 2.5→29.22 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.56 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 360 4.65 %
Rwork0.2117 7387 -
obs0.2143 7747 82.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.71 Å2 / Biso mean: 47.4535 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: final / Resolution: 2.5→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 35 6 1633
Biso mean--66.49 25.6 -
Num. residues----198
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 (%)
2.5-2.860.2972720.26431395146748
2.86-3.610.31821500.23912899304999
3.61-29.220.23141380.186230933231100
Refinement TLS params.Method: refined / Origin x: 4.5557 Å / Origin y: 10.8511 Å / Origin z: -23.2557 Å
111213212223313233
T0.1263 Å2-0.0627 Å20.0918 Å2-0.2793 Å20.1396 Å2--0.2588 Å2
L2.3228 °20.2164 °20.3664 °2-1.038 °20.2091 °2--3.1907 °2
S-0.1272 Å °0.5349 Å °0.5054 Å °-0.1453 Å °-0.0602 Å °0.1651 Å °-0.5992 Å °0.4355 Å °-0.1855 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 226
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allD1
4X-RAY DIFFRACTION1allE1 - 3
5X-RAY DIFFRACTION1allB1 - 6
6X-RAY DIFFRACTION1allF1

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