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- PDB-8j4n: Crystal Structure of the Acinetobacter baumannii LysR family regu... -

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Basic information

Entry
Database: PDB / ID: 8j4n
TitleCrystal Structure of the Acinetobacter baumannii LysR family regulator AceR effector-binding domain (APO FORM)
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
Bacterial regulatory helix-turn-helix protein, lysR family protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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


Theoretical massNumber of molelcules
Total (without water)68,3382
Polymers68,3382
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-12 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.520, 101.219, 57.970
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.66 Å3/Da / Density % sol: 26.08 %
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: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.23→61.54 Å / Num. obs: 22957 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.043 / Rrim(I) all: 0.094 / Net I/σ(I): 12.3
Reflection shellResolution: 2.23→2.35 Å / Rmerge(I) obs: 0.703 / Num. unique obs: 3285 / CC1/2: 0.787 / Rpim(I) all: 0.364 / Rrim(I) all: 0.794 / % possible all: 99.9

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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: 2.23→42.38 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1095 4.78 %
Rwork0.1976 --
obs0.1995 22912 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 0 79 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043293
X-RAY DIFFRACTIONf_angle_d0.744463
X-RAY DIFFRACTIONf_dihedral_angle_d6.066422
X-RAY DIFFRACTIONf_chiral_restr0.048505
X-RAY DIFFRACTIONf_plane_restr0.007568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.330.35521440.27072672X-RAY DIFFRACTION100
2.33-2.450.30681390.24452674X-RAY DIFFRACTION100
2.45-2.60.22791450.22442694X-RAY DIFFRACTION100
2.6-2.80.24621240.21252709X-RAY DIFFRACTION100
2.8-3.090.30061270.22412721X-RAY DIFFRACTION100
3.09-3.530.27391420.20462714X-RAY DIFFRACTION99
3.53-4.450.1841430.16582739X-RAY DIFFRACTION99
4.45-42.380.21831310.18192894X-RAY DIFFRACTION99
Refinement TLS params.

S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6203-0.05490.26540.992-0.21182.322-0.02960.0727-0.1026-0.05320.00810.00690.15290.05120.17840.0076-0.0070.2016-0.01580.2321-21.611119.8937-0.5325
20.750.5276-0.81461.232-0.61461.9370.0204-0.04430.14250.14860.03630.1179-0.1385-0.08160.18010.0174-0.02570.176-0.02490.2116-24.458340.31735.0465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 91:295)
2X-RAY DIFFRACTION2(chain B and resseq 93:293)

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