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- PDB-9iyz: Crystal Structure of the Acinetobacter baumannii LysR family regu... -

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Basic information

Entry
Database: PDB / ID: 9iyz
TitleCrystal Structure of the Acinetobacter baumannii LysR family regulator AceR DNA-binding domain (P321)
ComponentsHTH-type transcriptional regulator AceR
KeywordsDNA BINDING PROTEIN / LysR family regulator / DNA-binding domain / TRANSCRIPTION
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: 1.99 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 the Acinetobacter baumannii LysR family regulator AceR DNA-binding domain (P321)
Authors: Ma, J.M. / Ge, H.H. / Wang, N.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 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


Theoretical massNumber of molelcules
Total (without water)30,2063
Polymers30,2063
Non-polymers00
Water1,964109
1
A: HTH-type transcriptional regulator AceR
C: HTH-type transcriptional regulator AceR


Theoretical massNumber of molelcules
Total (without water)20,1372
Polymers20,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-22 kcal/mol
Surface area9080 Å2
MethodPISA
2
B: HTH-type transcriptional regulator AceR

B: HTH-type transcriptional regulator AceR


Theoretical massNumber of molelcules
Total (without water)20,1372
Polymers20,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.140, 87.140, 73.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein HTH-type transcriptional regulator AceR


Mass: 10068.587 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Gene: aceR, A1S_2064 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DUU5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion
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: 1.712→75.004 Å / Num. obs: 21957 / % possible obs: 99.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 34.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.036 / Rrim(I) all: 0.119 / Net I/σ(I): 10.5
Reflection shellResolution: 1.712→1.742 Å / Rmerge(I) obs: 0.904 / Num. unique obs: 5064 / CC1/2: 0.805 / Rpim(I) all: 0.377 / Rrim(I) all: 0.983

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→43.57 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1974 8.99 %RANDOM
Rwork0.2177 ---
obs0.2215 21957 97.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 0 109 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071977
X-RAY DIFFRACTIONf_angle_d0.9642664
X-RAY DIFFRACTIONf_dihedral_angle_d5.558258
X-RAY DIFFRACTIONf_chiral_restr0.05314
X-RAY DIFFRACTIONf_plane_restr0.007339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.38491370.29691326X-RAY DIFFRACTION92
2.04-2.10.29941340.24661340X-RAY DIFFRACTION94
2.1-2.160.29521310.23221384X-RAY DIFFRACTION95
2.16-2.230.28171380.23781391X-RAY DIFFRACTION97
2.23-2.310.28121380.24881391X-RAY DIFFRACTION97
2.31-2.40.32451400.24131411X-RAY DIFFRACTION98
2.4-2.510.28291460.2531419X-RAY DIFFRACTION98
2.51-2.640.30921400.22571449X-RAY DIFFRACTION99
2.64-2.810.27571430.2451439X-RAY DIFFRACTION99
2.81-3.020.28651430.24061438X-RAY DIFFRACTION99
3.02-3.330.31331480.24011467X-RAY DIFFRACTION100
3.33-3.80.24151410.1881468X-RAY DIFFRACTION100
3.81-4.790.20991420.18141495X-RAY DIFFRACTION100
4.8-43.570.21241530.20471565X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -29.4107 Å / Origin y: 6.9038 Å / Origin z: 17.692 Å
111213212223313233
T0.2428 Å20.0083 Å2-0.0177 Å2-0.1997 Å2-0.029 Å2--0.2288 Å2
L1.1744 °2-0.9158 °20.4792 °2-0.8412 °2-0.3948 °2--0.2999 °2
S0.0929 Å °0.1251 Å °-0.0312 Å °-0.1362 Å °-0.1025 Å °0.0692 Å °-0.008 Å °0.1065 Å °-0.002 Å °
Refinement TLS groupSelection details: all

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