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- PDB-9kpr: Crystal structure of a allulose transcriptional regulator from Ag... -

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Basic information

Entry
Database: PDB / ID: 9kpr
TitleCrystal structure of a allulose transcriptional regulator from Agrobacterium fabrum
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION / catalysis
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Periplasmic binding protein / Periplasmic binding protein domain / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
: / Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsWei, H.L. / Dong, Q.Z. / Liu, W.D. / Yang, J.G. / Sun, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: to be published
Title: Crystal structure of a allulose transcriptional regulator from Agrobacterium fabrum
Authors: Wei, H.L. / Dong, Q.Z. / Liu, W.D. / Yang, J.G. / Sun, Y.X.
History
DepositionNov 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3704
Polymers79,0102
Non-polymers3602
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-34 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.109, 113.109, 210.058
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transcriptional regulator, LacI family


Mass: 39504.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: Atu4743
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A9CH24
#2: Chemical ChemComp-A1EGE / D-Allulose


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 4.25 Å3/Da / Density % sol: 71.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0, 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979191 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 2.53→79.98 Å / Num. obs: 46358 / % possible obs: 100 % / Redundancy: 27.7 % / CC1/2: 0.994 / Χ2: 0.84 / Net I/σ(I): 8.4
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 29 % / Num. unique obs: 3365 / CC1/2: 0.65 / Χ2: 0.76

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.261 2313 -
Rwork0.231 --
obs-46358 99.5 %
Refinement stepCycle: LAST / Resolution: 2.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 0 194 4585
LS refinement shellResolution: 2.53→2.6 Å /
RfactorNum. reflection
Rfree0.424 -
Rwork0.391 -
obs-3365

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