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- PDB-9isw: Crystal structure of AlkR (VanR), a GntR family transcriptional r... -

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Basic information

Entry
Database: PDB / ID: 9isw
TitleCrystal structure of AlkR (VanR), a GntR family transcriptional regulator
ComponentsTranscriptional regulator
KeywordsDNA BINDING PROTEIN / a GntR family transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLiang, R. / Peng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370107 China
CitationJournal: To Be Published
Title: Crystal structure of AlkR (VanR), a GntR family transcriptional regulator
Authors: Liang, R. / Peng, W.
History
DepositionJul 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)25,1031
Polymers25,1031
Non-polymers00
Water1,874104
1
A: Transcriptional regulator

A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)50,2062
Polymers50,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area2030 Å2
ΔGint-9 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.544, 122.544, 61.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-322-

HOH

31A-334-

HOH

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Components

#1: Protein Transcriptional regulator / AlkR / GntR family transcriptional regulator


Mass: 25102.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: mcbR_1, ALP65_03525, CAZ10_35765, GUL26_35315, IPC1295_04330, NCTC13621_01527, PAERUG_P19_London_7_VIM_2_05_10_00190
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q939
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Potassium thiocyanate, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.86→40.83 Å / Num. obs: 19920 / % possible obs: 99.8 % / Redundancy: 25.6 % / Biso Wilson estimate: 21.17 Å2 / CC1/2: 0.994 / Net I/σ(I): 19
Reflection shellResolution: 1.86→1.89 Å / Num. unique obs: 972 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000v7.21data scaling
PDB_EXTRACTV4.1data extraction
HKL-3000v7.21data reduction
PHENIXv1.17.1-3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→40.83 Å / SU ML: 0.2087 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 1042 5.23 %
Rwork0.1978 18878 -
obs0.1992 19920 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.78 Å2
Refinement stepCycle: LAST / Resolution: 1.86→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 0 104 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681707
X-RAY DIFFRACTIONf_angle_d0.76182307
X-RAY DIFFRACTIONf_chiral_restr0.0482266
X-RAY DIFFRACTIONf_plane_restr0.005304
X-RAY DIFFRACTIONf_dihedral_angle_d31.7288649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.960.27831290.22592657X-RAY DIFFRACTION99.46
1.96-2.080.24191470.1992652X-RAY DIFFRACTION99.96
2.08-2.240.23241680.1832640X-RAY DIFFRACTION100
2.24-2.460.19281310.18162693X-RAY DIFFRACTION100
2.46-2.820.21511560.19332686X-RAY DIFFRACTION100
2.82-3.550.23281450.19512725X-RAY DIFFRACTION100
3.55-40.830.21351660.20642825X-RAY DIFFRACTION99.27

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