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- PDB-3o75: Crystal structure of Cra transcriptional dual regulator from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3o75
TitleCrystal structure of Cra transcriptional dual regulator from Pseudomonas putida in complex with fructose 1-phosphate'
ComponentsFructose transport system repressor FruR
KeywordsTRANSCRIPTION / Dual transcription regulator / DNA
Function / homology
Function and homology information


response to fructose / protein-DNA complex / sequence-specific DNA binding / regulation of DNA-templated transcription
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 / Response regulator ...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 / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-O-phosphono-beta-D-fructofuranose / Catabolite repressor-activator, DNA-binding transcriptional dual regulator
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChavarria, M. / Santiago, C. / Platero, R. / Krell, T. / Casasnovas, J.M. / de Lorenzo, V.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Fructose 1-phosphate is the preferred effector of the metabolic regulator Cra of Pseudomonas putida
Authors: Chavarria, M. / Santiago, C. / Platero, R. / Krell, T. / Casasnovas, J.M. / de Lorenzo, V.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose transport system repressor FruR
B: Fructose transport system repressor FruR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4224
Polymers59,9012
Non-polymers5202
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-8 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.711, 120.220, 61.860
Angle α, β, γ (deg.)90.000, 107.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fructose transport system repressor FruR / Cra transcriptional dual regulator


Mass: 29950.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: ECK0081 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q88PQ6
#2: Sugar ChemComp-F1X / 1-O-phosphono-beta-D-fructofuranose / beta D-Fructose 1-phosphate / 1-O-phosphono-beta-D-fructose / 1-O-phosphono-D-fructose / 1-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FULL SEQUENCE OF THIS PROTEIN USED FOR CRYSTALLIZATION IS ...THE FULL SEQUENCE OF THIS PROTEIN USED FOR CRYSTALLIZATION IS MGSSHHHHHHSSGVRGSHMKLSDIARLAGVSVTTASYVINGKAEQQRISNST VERVRAVVEAHGFTPNPQAAGLRSRHTRTLGFILPDLENPSYARIAKQLEQGARARGYQL LIASSDDQPDSERQLQQLFRARRCDALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPA HFCSVISDDRDASRQLAASLLSSAPRSIALIGARPELSVSQARAGGFDEALQGYTGEVRR YQGEAFSRECGQRLMQQLIDDLGGLPDALVTTSYVLLQGVFDTLQARPVDSRQLQL GTFGDNQLLDFLPLPVNAMAQQHGQIAATALELALAAIEEKRYEPGVHAVGRTFKQ RISVA. HOWEVER, RESIDUES AT N-TERMINUS SEEM TO BE DEGRADED IN CRYSTAL AND THE ACTUAL CRYSTALLIZED PROTEIN SEQUENCE MAY BE SHORTER. IN FACT MASS SPECTROMETRY COULD ONLY SHOW A PEAK OF 30.4KDA WEIGHT. ONLY THE ORDERED PART OF THE PROTEIN BY THE ELECTRON DENSITY MAP IS REPORTED IN SEQRES RECORDS. THE FIRST 18 RESIDUES MGSSHHHHHHSSGVRGSH ARE EXPRESSION TAG SEQUENCE.

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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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Mes pH 6.5, 0.2M NaAc, 15 % PEG 8000, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→42 Å / Num. obs: 23340 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.6 / Num. measured all: 79179

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O74

3o74


Resolution: 2.3→14.944 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8293 / SU ML: 0.29 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 1130 5.12 %
Rwork0.1837 --
obs0.1858 22057 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.172 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 142.59 Å2 / Biso mean: 50.4763 Å2 / Biso min: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1-12.3008 Å2-0 Å24.866 Å2
2---10.9794 Å20 Å2
3----1.3214 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 32 107 4325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034293
X-RAY DIFFRACTIONf_angle_d0.8765819
X-RAY DIFFRACTIONf_chiral_restr0.053649
X-RAY DIFFRACTIONf_plane_restr0.003784
X-RAY DIFFRACTIONf_dihedral_angle_d22.8212705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40430.28991310.25142404253587
2.4043-2.53050.28011340.22532466260090
2.5305-2.68820.27711380.21082562270092
2.6882-2.89430.25761210.20822619274095
2.8943-3.18310.2341470.19612663281097
3.1831-3.63780.23841490.18142725287499
3.6378-4.56160.18211610.15542733289499
4.5616-14.94440.18161490.15222755290498
Refinement TLS params.Method: refined / Origin x: 2.8116 Å / Origin y: -6.7187 Å / Origin z: 3.2438 Å
111213212223313233
T0.0527 Å2-0.0098 Å20.0179 Å2-0.1487 Å2-0.0001 Å2--0.0834 Å2
L0.8869 °2-0.8445 °20.4851 °2-3.2806 °2-0.8809 °2--0.7926 °2
S-0.0392 Å °0.0417 Å °-0.009 Å °0.1253 Å °0.0161 Å °0.1208 Å °-0.0347 Å °0.0239 Å °0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA60 - 329
2X-RAY DIFFRACTION1allB60 - 329
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allA1
5X-RAY DIFFRACTION1allB1 - 359

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