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- PDB-3hfi: The crystal structure of the putative regulator from Escherichia ... -

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Basic information

Entry
Database: PDB / ID: 3hfi
TitleThe crystal structure of the putative regulator from Escherichia coli CFT073
ComponentsPutative regulator
Keywordsstructural genomics / unknown function / regulator / structural geonomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. ...UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative regulator / Putative regulator
Similarity search - Component
Biological speciesEscherichia coli O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative regulator from Escherichia coli CFT073
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative regulator


Theoretical massNumber of molelcules
Total (without water)19,6611
Polymers19,6611
Non-polymers00
Water72140
1
A: Putative regulator

A: Putative regulator


Theoretical massNumber of molelcules
Total (without water)39,3232
Polymers39,3232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.656, 103.656, 58.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

DetailsThis protein exists as dimer. The second part of the biological assembly is generated by the axis: Y,X,-Z

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Components

#1: Protein Putative regulator


Mass: 19661.430 Da / Num. of mol.: 1 / Fragment: residues 82-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: CFT073 / Gene: c4276, GI:26250098 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8FCM7, UniProt: A0A0H2VBL3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na(OAC), 3.5M NaFormate, 1/600 CHYMOTRYPSIN, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→89.8 Å / Num. all: 9339 / Num. obs: 9325 / % possible obs: 99.85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 27.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 51.9
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 26.6 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 3.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→89.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.14 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.202
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25558 471 4.8 %RANDOM
Rwork0.20058 ---
obs0.20335 9325 99.85 %-
all-9339 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.16 Å20 Å2
2---0.31 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→89.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 0 40 1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221138
X-RAY DIFFRACTIONr_bond_other_d0.0010.02805
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9741537
X-RAY DIFFRACTIONr_angle_other_deg1.05731948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8075136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50123.27658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20515208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1171512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
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_it1.2021.5682
X-RAY DIFFRACTIONr_mcbond_other0.2361.5275
X-RAY DIFFRACTIONr_mcangle_it2.24621106
X-RAY DIFFRACTIONr_scbond_it3.2653456
X-RAY DIFFRACTIONr_scangle_it5.6614.5431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 22 -
Rwork0.259 683 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: 40.897 Å / Origin y: 46.583 Å / Origin z: 3.807 Å
111213212223313233
T0.1736 Å20.0536 Å2-0.0062 Å2-0.182 Å20.0098 Å2--0.2744 Å2
L5.4407 °2-1.9552 °20.8133 °2-3.2844 °20.5777 °2--3.0475 °2
S-0.086 Å °-0.0324 Å °0.3146 Å °0.0127 Å °0.0306 Å °-0.4446 Å °-0.4055 Å °-0.0905 Å °0.0554 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 60
2X-RAY DIFFRACTION1A61 - 90
3X-RAY DIFFRACTION1A91 - 120
4X-RAY DIFFRACTION1A121 - 157

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