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- PDB-7doa: Crystal structure of Catabolite repressor acivator from E. coli i... -

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Basic information

Entry
Database: PDB / ID: 7doa
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 / 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
Catabolite repressor/activator
Similarity search - Component
Biological speciesEscherichia coli O6:K15:H31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNeetu, N. / Katiki, M. / Kumar, P.
CitationJournal: To Be Published
Title: Crystal structure of Catabolite repressor acivator from E. coli in complex with HEPES
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)82,4306
Polymers81,6232
Non-polymers8074
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.932, 43.341, 108.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-507-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 60 - 333 / Label seq-ID: 83 - 356

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.50264, 0.864488, 0.003721), (0.864288, -0.502421, -0.024069), (-0.018937, 0.015314, -0.999703)14.89539, -26.235861, -53.897598

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Components

#1: Protein Catabolite repressor/activator / Fructose repressor


Mass: 40811.289 Da / Num. of mol.: 2
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.79 Å3/Da / Density % sol: 31.42 %
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: 2.7→40.91 Å / Num. obs: 16445 / % possible obs: 97.78 % / Redundancy: 0.08726 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 3740 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
SCALEPACKdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IKS

2iks


Resolution: 2.7→40.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 49.063 / SU ML: 0.446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 824 5 %RANDOM
Rwork0.2172 ---
obs0.2206 15622 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.87 Å2 / Biso mean: 74.035 Å2 / Biso min: 41.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å20 Å2
2--2.17 Å20 Å2
3----1.53 Å2
Refinement stepCycle: final / Resolution: 2.7→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4436 0 51 63 4550
Biso mean--89 65.79 -
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194606
X-RAY DIFFRACTIONr_angle_refined_deg2.0151.9816255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45122.941238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.13415774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6691554
X-RAY DIFFRACTIONr_chiral_restr0.1310.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213542
Refine LS restraints NCS

Ens-ID: 1 / Number: 16498 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 58 -
Rwork0.372 1111 -
all-1169 -
obs--98.57 %
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)
14.35111.76660.00781.8701-0.03642.73230.01690.0747-0.0821-0.03020.1076-0.0268-0.0139-0.0239-0.12450.47580.0443-0.01720.1532-0.01950.03411.333-7.454-39.734
23.58160.87210.39491.5423-0.18863.16750.0877-0.09670.09140.09540.097-0.01890.60910.366-0.18480.64850.1175-0.04710.2083-0.04610.01839.132-20.99-14.665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 333
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B60 - 333
4X-RAY DIFFRACTION2B401

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