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- PDB-7dob: Crystal structure of Catabolite repressor activator (Apo) -

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Basic information

Entry
Database: PDB / ID: 7dob
TitleCrystal structure of Catabolite repressor activator (Apo)
ComponentsCatabolite repressor/activator
KeywordsGENE REGULATION / transcription factor / DNA BINDING PROTEIN
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 O6:K15:H31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNeetu, N. / Katiki, M. / Kumar, P.
CitationJournal: To Be Published
Title: Crystal structure of Catabolite repressor activator (Apo)
Authors: Neetu, N. / Katiki, M. / Kumar, P.
History
DepositionDec 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catabolite repressor/activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0555
Polymers40,8111
Non-polymers2434
Water1,00956
1
A: Catabolite repressor/activator
hetero molecules

A: Catabolite repressor/activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,10910
Polymers81,6232
Non-polymers4878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area4870 Å2
ΔGint-25 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.577, 102.577, 160.328
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

21A-550-

HOH

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Components

#1: Protein Catabolite repressor/activator / Fructose repressor


Mass: 40811.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:K15:H31 (strain 536 / UPEC) (bacteria)
Strain: 536 / UPEC / Gene: ECP_0082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A454A0X5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.3M MgCl2, 0.1M MES, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.4→42.8 Å / Num. obs: 12911 / % possible obs: 99.36 % / Redundancy: 8.7 % / CC1/2: 0.99 / Net I/σ(I): 13.84
Reflection shellResolution: 2.4→2.48 Å / Num. unique obs: 1268 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IKS

2iks


Resolution: 2.4→36.535 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2728 642 4.98 %
Rwork0.2266 12239 -
obs0.2287 12881 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.99 Å2 / Biso mean: 67.4387 Å2 / Biso min: 26.19 Å2
Refinement stepCycle: final / Resolution: 2.4→36.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 14 56 2310
Biso mean--79.92 66.91 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042310
X-RAY DIFFRACTIONf_angle_d0.73133
X-RAY DIFFRACTIONf_chiral_restr0.045344
X-RAY DIFFRACTIONf_plane_restr0.005415
X-RAY DIFFRACTIONf_dihedral_angle_d11.291972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.58530.39941270.3856241299
2.5853-2.84530.35591360.3296240799
2.8453-3.25680.34991380.27692409100
3.2568-4.10240.26581170.1981244699
4.1024-36.5350.20591240.18732565100
Refinement TLS params.Method: refined / Origin x: 14.172 Å / Origin y: 38.3312 Å / Origin z: -15.1159 Å
111213212223313233
T0.361 Å20.0044 Å2-0.0237 Å2-0.4957 Å20.0083 Å2--0.3721 Å2
L4.7711 °2-1.8794 °2-3.0398 °2-1.6947 °20.6312 °2--3.5198 °2
S-0.0531 Å °0.576 Å °-0.2067 Å °0.1285 Å °-0.0366 Å °0.3517 Å °0.0245 Å °-0.9146 Å °0.0372 Å °
Refinement TLS groupSelection details: all

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