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- PDB-8wp7: Crystal structure of a TetR family regulator AmvR from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 8wp7
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: 1.91 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: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2922
Polymers22,1461
Non-polymers1451
Water2,576143
1
A: TetR family transcriptional regulator
hetero molecules

A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5834
Polymers44,2932
Non-polymers2902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area3520 Å2
ΔGint-4 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.268, 70.318, 50.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein TetR family transcriptional regulator


Mass: 22146.275 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 289 K / Method: evaporation
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: Sep 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.91→47.44 Å / Num. obs: 18423 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 30.67 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.036 / Rrim(I) all: 0.11 / Net I/σ(I): 12.3
Reflection shellResolution: 1.91→2.01 Å / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2641 / Rpim(I) all: 0.226 / Rrim(I) all: 0.527

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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: 1.91→35.16 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 878 4.77 %
Rwork0.1917 --
obs0.1932 18389 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 10 143 1656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031535
X-RAY DIFFRACTIONf_angle_d0.5642064
X-RAY DIFFRACTIONf_dihedral_angle_d5.41207
X-RAY DIFFRACTIONf_chiral_restr0.04231
X-RAY DIFFRACTIONf_plane_restr0.003267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.030.29811360.24872850X-RAY DIFFRACTION99
2.03-2.180.2481420.21012871X-RAY DIFFRACTION100
2.18-2.40.23381650.19092892X-RAY DIFFRACTION100
2.4-2.750.24821360.2082880X-RAY DIFFRACTION100
2.75-3.460.25731510.20332935X-RAY DIFFRACTION100
3.46-35.160.18131480.17053083X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.8677 Å / Origin y: 27.2457 Å / Origin z: 11.5422 Å
111213212223313233
T0.1795 Å2-0.0153 Å2-0.008 Å2-0.219 Å20.0318 Å2--0.2022 Å2
L0.4021 °20.5067 °2-0.4993 °2-0.784 °2-0.5654 °2--0.64 °2
S-0.025 Å °0.0807 Å °0.0205 Å °-0.0397 Å °0.1197 Å °0.0999 Å °0.0142 Å °-0.2298 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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