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- PDB-3o74: Crystal structure of Cra transcriptional dual regulator from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3o74
TitleCrystal structure of Cra transcriptional dual regulator from Pseudomonas putida
ComponentsFructose transport system repressor FruR
KeywordsTRANSCRIPTION / Dual transcriptional 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
Catabolite repressor-activator, DNA-binding transcriptional dual regulator
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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

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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)60,2734
Polymers60,0892
Non-polymers1842
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-9 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.309, 118.506, 61.834
Angle α, β, γ (deg.)90.000, 107.130, 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: 30044.514 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FULL SEQUENCE OF THIS PROTEIN USED FOR CRYSTALLIZATION IS (MSE)GSSHHHHHHSSGVRGSH(MSE) ...THE FULL SEQUENCE OF THIS PROTEIN USED FOR CRYSTALLIZATION IS (MSE)GSSHHHHHHSSGVRGSH(MSE)KLSDIARLAGVSVTTASYVINGKAEQQRISNST VERVRAVVEAHGFTPNPQAAGLRSRHTRTLGFILPDLENPSYARIAKQLEQGARARGYQL LIASSDDQPDSERQLQQLFRARRCDALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPA HFCSVISDDRDASRQLAASLLSSAPRSIALIGARPELSVSQARAGGFDEALQGYTGEVRR YQGEAFSRECGQRL(MSE)QQLIDDLGGLPDALVTTSYVLLQGVFDTLQARPVDSRQLQL GTFGDNQLLDFLPLPVNA(MSE)AQQHGQIAATALELALAAIEEKRYEPGVHAVGRTFKQ 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 (MSE)GSSHHHHHHSSGVRGSH 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: 2.17 Å3/Da / Density % sol: 43.42 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Mes pH 6.5, 0.2M NaAc, 15% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2→59 Å / Num. obs: 66131 / % possible obs: 99.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.083 / Num. measured all: 254515

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→14.928 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.844 / SU ML: 0.27 / σ(F): 0.02 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflection
Rfree0.2179 3320 5.02 %
Rwork0.1838 --
obs0.1856 66122 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.413 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 118.85 Å2 / Biso mean: 40.8265 Å2 / Biso min: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1-7.0752 Å2-0 Å23.8227 Å2
2---6.1698 Å20 Å2
3----0.9053 Å2
Refinement stepCycle: LAST / Resolution: 2→14.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 12 175 4380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034287
X-RAY DIFFRACTIONf_angle_d0.715806
X-RAY DIFFRACTIONf_chiral_restr0.048646
X-RAY DIFFRACTIONf_plane_restr0.003787
X-RAY DIFFRACTIONf_dihedral_angle_d21.9172708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02850.23551220.23842393251589
2.0285-2.05870.28931260.22642484261090
2.0587-2.09080.23751280.23622498262693
2.0908-2.1250.26671210.2182483260493
2.125-2.16150.2431290.22782581271095
2.1615-2.20070.29191080.22062637274595
2.2007-2.24290.27541380.21412503264196
2.2429-2.28850.28291600.20542585274597
2.2885-2.33810.2621540.20952594274896
2.3381-2.39230.2761190.21352654277397
2.3923-2.45190.2261380.20442643278198
2.4519-2.51780.26061280.20262688281699
2.5178-2.59160.19161560.19362600275698
2.5916-2.67480.25511220.20512725284799
2.6748-2.76980.28771240.20242639276399
2.7698-2.87990.21171460.20022711285799
2.8799-3.010.25121390.19272669280899
3.01-3.16720.17991210.194727102831100
3.1672-3.36350.18821590.188826932852100
3.3635-3.61980.20511540.160626792833100
3.6198-3.97780.20281980.160826262824100
3.9778-4.53920.17131360.145227082844100
4.5392-5.66640.18481440.150926962840100
5.6664-14.92820.20171500.16182603275396
Refinement TLS params.Method: refined / Origin x: 11.9019 Å / Origin y: -4.459 Å / Origin z: 33.4317 Å
111213212223313233
T0.0801 Å2-0.0149 Å20.0226 Å2-0.1296 Å20.0013 Å2--0.1055 Å2
L0.6784 °2-0.689 °20.3601 °2-2.0997 °2-0.5489 °2--0.6289 °2
S-0.0812 Å °-0.018 Å °0.0446 Å °0.0617 Å °0.1024 Å °-0.0391 Å °-0.0564 Å °-0.0218 Å °-0.0159 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA60 - 329
2X-RAY DIFFRACTION1allB60 - 330
3X-RAY DIFFRACTION1allB301 - 332
4X-RAY DIFFRACTION1allA301 - 332
5X-RAY DIFFRACTION1allB - A1 - 388

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