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

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Basic information

Entry
Database: PDB / ID: 8jff
TitleCrystal structure of Catabolite repressor acivator from E. coli in complex with HEPES
ComponentsCatabolite repressor/activator
KeywordsGENE REGULATION / Cra / HEPES / DNA BINDING PROTEIN
Function / homology
Function and homology information


response to fructose / regulation of DNA-templated transcription / DNA binding
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
Catabolite repressor/activator
Similarity search - Component
Biological speciesEscherichia coli 536 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsNeetu, N. / Katiki, M. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical Research 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 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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)76,5794
Polymers76,1032
Non-polymers4772
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint3 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.330, 108.900, 123.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#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
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 / 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: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.89→108.9 Å / Num. obs: 12352 / % possible obs: 90.1 % / Redundancy: 1.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Net I/σ(I): 12.5
Reflection shellResolution: 2.89→3.06 Å / Rmerge(I) obs: 0.341 / Num. unique obs: 2133 / CC1/2: 0.883 / Rpim(I) all: 0.341

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→54.51 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.894 / SU B: 42 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2827 590 4.8 %RANDOM
Rwork0.22398 ---
obs0.22678 11741 89.48 %-
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 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--0.72 Å20 Å2
3----2.3 Å2
Refinement stepCycle: 1 / Resolution: 2.89→54.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 30 42 4512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124566
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164364
X-RAY DIFFRACTIONr_angle_refined_deg0.7461.6666198
X-RAY DIFFRACTIONr_angle_other_deg0.271.57310012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.751554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35210776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0360.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021110
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_it1.1955.5082190
X-RAY DIFFRACTIONr_mcbond_other1.1955.5082190
X-RAY DIFFRACTIONr_mcangle_it2.1429.9052734
X-RAY DIFFRACTIONr_mcangle_other2.1429.9052735
X-RAY DIFFRACTIONr_scbond_it0.9575.7332376
X-RAY DIFFRACTIONr_scbond_other0.9575.7332377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.79110.4873465
X-RAY DIFFRACTIONr_long_range_B_refined3.85852.44975
X-RAY DIFFRACTIONr_long_range_B_other3.85852.44976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.89→2.963 Å
RfactorNum. reflection% reflection
Rfree0.347 45 -
Rwork0.314 914 -
obs--98.97 %
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)
10.5690.09351.12141.9782-0.04362.23640.0531-0.02730.0282-0.0461-0.1337-0.08880.0932-0.03470.08060.0087-0.0008-0.02620.1663-0.02470.27814.195514.88081.2417
20.2985-0.14580.56922.27620.41341.3118-0.030.1751-0.01020.3347-0.12580.6468-0.0090.32110.15590.0554-0.04360.11830.1096-0.06020.44030.728339.55559.2055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 401
2X-RAY DIFFRACTION2B60 - 405

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