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

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Basic information

Entry
Database: PDB / ID: 8wpa
TitleCrystal Structure of the Acinetobacter baumannii LysR family regulator AceR DNA-binding domain (H32)
ComponentsHTH-type transcriptional regulator AceR
KeywordsTRANSCRIPTION / LysR family regulator / effector-binding domain
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm
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
HTH-type transcriptional regulator AceR
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMa, J.M. / Ge, H.H. / Wang, N.
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
DepositionOct 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator AceR
B: HTH-type transcriptional regulator AceR
C: HTH-type transcriptional regulator AceR
D: HTH-type transcriptional regulator AceR


Theoretical massNumber of molelcules
Total (without water)43,4744
Polymers43,4744
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.130, 86.130, 299.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-142-

HOH

21C-152-

HOH

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Components

#1: Protein
HTH-type transcriptional regulator AceR


Mass: 10868.468 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: aceR / Production host: Escherichia coli (E. coli) / References: UniProt: P0DUU5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.08 M Magnesium acetate tetrahydrate, 0.1 M Sodium HEPES pH 7.5, 16% v/v PEG Smear Low

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.72→99.93 Å / Num. obs: 45778 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.042 / Rrim(I) all: 0.121 / Net I/σ(I): 11
Reflection shellResolution: 1.723→1.753 Å / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2246 / CC1/2: 0.717 / Rpim(I) all: 0.37 / Rrim(I) all: 0.898 / % possible all: 99.9

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Processing

Software
NameClassification
PDB-REDOrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→72.49 Å / SU B: 2.386 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22662 2331 5.1 %RANDOM
Rwork0.21136 ---
obs0.21217 43446 99.9 %-
Displacement parametersBiso mean: 25.931 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.72→72.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 0 242 2919

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