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- PDB-8j4o: Crystal Structure of the Acinetobacter baumannii LysR family regu... -

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Basic information

Entry
Database: PDB / ID: 8j4o
TitleCrystal Structure of the Acinetobacter baumannii LysR family regulator AceR effector-binding domain with Spermidine
ComponentsBacterial regulatory helix-turn-helix protein, lysR family protein
KeywordsTRANSCRIPTION / LysR family regulator / effector-binding domain
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
SPERMIDINE / Bacterial regulatory helix-turn-helix protein, lysR family protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMa, J.M. / Ge, H.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071215 China
CitationJournal: To Be Published
Title: Crystal Structure of Acinetobacter baumannii LysR family regulator AceR effector binding domain (apo)
Authors: Ma, J.M. / Ge, H.H.
History
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial regulatory helix-turn-helix protein, lysR family protein
B: Bacterial regulatory helix-turn-helix protein, lysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4843
Polymers68,3382
Non-polymers1451
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-6 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.795, 100.894, 55.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bacterial regulatory helix-turn-helix protein, lysR family protein / LysR family regulator AceR


Mass: 34169.141 Da / Num. of mol.: 2 / Fragment: effector-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: cynR_1 / Production host: Escherichia coli (E. coli) / References: UniProt: V5VDR8
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 1.58 Å3/Da / Density % sol: 22.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion / Details: 1.5 M Ammonium sulfate, 0.1 M Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.966→61.108 Å / Num. obs: 29903 / % possible obs: 94.6 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.046 / Rrim(I) all: 0.126 / Net I/σ(I): 13.2
Reflection shellResolution: 1.966→2 Å / Rmerge(I) obs: 1.308 / Mean I/σ(I) obs: 2 / Num. unique obs: 1561 / CC1/2: 0.688 / Rpim(I) all: 0.522 / Rrim(I) all: 1.411 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.97→55.85 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1438 4.81 %
Rwork0.1905 --
obs0.1919 29870 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→55.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3085 0 10 260 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043161
X-RAY DIFFRACTIONf_angle_d0.6864292
X-RAY DIFFRACTIONf_dihedral_angle_d6.923416
X-RAY DIFFRACTIONf_chiral_restr0.048494
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.040.31951420.242969X-RAY DIFFRACTION100
2.04-2.120.25711170.22812188X-RAY DIFFRACTION74
2.12-2.210.2991400.21352981X-RAY DIFFRACTION100
2.21-2.330.2895990.19952099X-RAY DIFFRACTION71
2.33-2.480.22091530.1982992X-RAY DIFFRACTION100
2.48-2.670.26111700.19422963X-RAY DIFFRACTION100
2.67-2.940.22951350.2032998X-RAY DIFFRACTION100
2.94-3.360.20931540.18663016X-RAY DIFFRACTION100
3.36-4.240.19831670.16683040X-RAY DIFFRACTION100
4.24-55.850.17871610.18693186X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.9075 Å / Origin y: 20.7777 Å / Origin z: 2.222 Å
111213212223313233
T0.0871 Å20.0089 Å2-0.0026 Å2-0.102 Å20.0024 Å2--0.1039 Å2
L0.069 °20.0074 °2-0.007 °2-0.2899 °20.24 °2--0.4745 °2
S-0.0187 Å °0.0047 Å °0.0013 Å °0.023 Å °0.0177 Å °0.0179 Å °0.0004 Å °0.0223 Å °-0 Å °
Refinement TLS groupSelection details: all

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