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- PDB-9ipt: Crystal structure of a TetR family regulator AmvR from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 9ipt
TitleCrystal structure of a TetR family regulator AmvR from Acinetobacter baumannii with spermidine bound
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / TetR family regulator / effector-binding domain
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
SPERMIDINE / TetR family transcriptional regulator
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 a TetR family regulator AmvR from Acinetobacter baumannii with spermidine bound
Authors: Ma, J.M. / Ge, H.H. / Wang, N.
History
DepositionJul 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5834
Polymers44,2932
Non-polymers2902
Water00
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)60.005, 65.510, 101.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TetR family transcriptional regulator


Mass: 22146.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ABCAM1_2317 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5YGI2
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2 M Sodium formate, 10% v/v Ethylene glycol, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14340 / % possible obs: 100 % / Redundancy: 11.43 % / Biso Wilson estimate: 53.2 Å2 / CC1/2: 0.9525 / CC star: 0.9878 / Rmerge(I) obs: 0.1731 / Rpim(I) all: 0.0541 / Net I/σ(I): 20.65
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 1.3857 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1022 / CC1/2: 0.5725 / CC star: 0.8533 / Rpim(I) all: 0.4961

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Processing

Software
NameVersionClassification
autoPXdata processing
PHASERphasing
PHENIX(1.19.2_4158: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.95 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 673 4.72 %
Rwork0.2285 --
obs0.2304 14245 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 20 0 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023045
X-RAY DIFFRACTIONf_angle_d0.4574098
X-RAY DIFFRACTIONf_dihedral_angle_d5.375413
X-RAY DIFFRACTIONf_chiral_restr0.033462
X-RAY DIFFRACTIONf_plane_restr0.003529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.36471230.35072640X-RAY DIFFRACTION99
2.69-2.960.35231370.28722676X-RAY DIFFRACTION100
2.96-3.390.32371260.27632690X-RAY DIFFRACTION99
3.39-4.270.2881420.2162719X-RAY DIFFRACTION100
4.27-29.950.21651450.19172847X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.1069 Å / Origin y: 0.2647 Å / Origin z: 14.6578 Å
111213212223313233
T0.5039 Å2-0.0058 Å20.0048 Å2-0.6036 Å2-0.0496 Å2--0.3189 Å2
L0.6699 °20.5573 °2-0.7095 °2-1.5314 °2-1.6957 °2--3.1614 °2
S0.0383 Å °-0.0156 Å °0.0282 Å °0.0303 Å °0.0789 Å °0.1283 Å °0.1251 Å °-0.0584 Å °-0.1006 Å °
Refinement TLS groupSelection details: all

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