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- PDB-8jfv: Crystal structure of Catabolite repressor acivator from E. coli i... -

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Basic information

Entry
Database: PDB / ID: 8jfv
TitleCrystal structure of Catabolite repressor acivator from E. coli in complex with sulisobenzone
ComponentsCatabolite repressor/activator
KeywordsTRANSCRIPTION / Transcription factor / bacterial / sulsiobenzone
Function / homology
Function and homology information


response to fructose / transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
: / PHOSPHATE ION / Catabolite repressor/activator
Similarity search - Component
Biological speciesEscherichia coli 536 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsNeetu, N. / Sharma, M. / Mahto, J.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchISRM/12(05)/2019 India
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Sulisobenzone is a potent inhibitor of the global transcription factor Cra.
Authors: Neetu, N. / Mahto, J.K. / Sharma, M. / Katiki, M. / Dhaka, P. / Roy, P. / Tomar, S. / Narayan, A. / Yernool, D. / Kumar, P.
History
DepositionMay 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catabolite repressor/activator
B: Catabolite repressor/activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8066
Polymers76,1032
Non-polymers7044
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-2 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.043, 109.241, 122.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Catabolite repressor/activator


Mass: 38051.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 536 (bacteria) / Gene: ECP_0082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A454A0X5

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Non-polymers , 5 types, 38 molecules

#2: Chemical ChemComp-I4Y / Sulisobenzone / 2-methoxy-4-oxidanyl-5-(phenylcarbonyl)benzenesulfonic acid


Mass: 308.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, MgCl2, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.973 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 3.05→43.08 Å / Num. obs: 11380 / % possible obs: 98.4 % / Redundancy: 1.8 % / CC1/2: 0.969 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.056 / Net I/σ(I): 17.6
Reflection shellResolution: 3.05→3.26 Å / Rmerge(I) obs: 0.395 / Num. unique obs: 2037 / CC1/2: 0.677 / Rpim(I) all: 0.395

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→43.08 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.89 / SU B: 67.492 / SU ML: 0.52 / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27746 594 5.2 %RANDOM
Rwork0.23404 ---
obs0.23645 10785 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.891 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0 Å2
2--2.03 Å20 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 3.05→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 45 34 4508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124569
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164350
X-RAY DIFFRACTIONr_angle_refined_deg0.7651.6716204
X-RAY DIFFRACTIONr_angle_other_deg0.2771.5759975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.445553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25110773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0370.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021111
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.285.3272186
X-RAY DIFFRACTIONr_mcbond_other1.285.3272186
X-RAY DIFFRACTIONr_mcangle_it2.3139.582729
X-RAY DIFFRACTIONr_mcangle_other2.3139.5792730
X-RAY DIFFRACTIONr_scbond_it0.9665.5272383
X-RAY DIFFRACTIONr_scbond_other0.9665.5272384
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.84310.1263476
X-RAY DIFFRACTIONr_long_range_B_refined4.35351.114827
X-RAY DIFFRACTIONr_long_range_B_other4.35351.114827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 35 -
Rwork0.382 773 -
obs--96.42 %
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5314-0.29470.82891.9246-0.02221.64130.01130.10530.11060.1771-0.11960.4622-0.00510.17870.10830.065-0.00980.11210.0266-0.01940.3329-21.066-14.9069.212
20.55520.06211.11651.50960.31072.32990.13830.00880.0305-0.0475-0.18450.06640.2308-0.00390.04620.12020.0466-0.03450.0472-0.04970.1639-7.419-39.6951.426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 333
2X-RAY DIFFRACTION2B61 - 333

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