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- PDB-3qfi: X-ray crystal structure of transcriptional regulator (EF0465) fro... -

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Basic information

Entry
Database: PDB / ID: 3qfi
TitleX-ray crystal structure of transcriptional regulator (EF0465) from Enterococcus faecalis, Northeast Structural Genomics Consortium Target EfR190
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / alpha-beta protein / transcriptional regulator
Function / homologyLCP protein / : / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / Transcriptional regulator
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hun, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray crystal structure of transcriptional regulator (EF0465) from Enterococcus faecalis, Northeast Structural Genomics Consortium Target EfR190
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hun, J.F. / Northeast Structural ...Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Wang, H. / Ciccosanti, C. / Mao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hun, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)33,7641
Polymers33,7641
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.214, 54.543, 99.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator


Mass: 33763.941 Da / Num. of mol.: 1 / Fragment: sequence database residues 42-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF0465, EF_0465 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q838I2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.9 Å3/Da / Density % sol: 35.2 %
Crystal growTemperature: 277 K / Method: microbatch under oil method / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT, Precipitation solution: 0.1M HEPES (pH 7.5), 40% PEG400, and 0.1M calcium acetate, microbatch under oil method, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97877 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 4, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 7395 / Num. obs: 6316 / % possible obs: 85.4 % / Observed criterion σ(F): 0.3 / Observed criterion σ(I): 0.3 / Redundancy: 4.3 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.078 / Net I/σ(I): 14.88
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 4.3 / Num. unique all: 465 / Rsym value: 0.125 / % possible all: 65.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNS1.2 & Xtalviewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKZ

3okz


Resolution: 2.71→19.87 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 406735.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 665 11 %RANDOM
Rwork0.201 ---
all0.205 7371 --
obs0.201 6045 82 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.0745 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å20 Å20 Å2
2---6.07 Å20 Å2
3---8.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.12 Å
Refinement stepCycle: LAST / Resolution: 2.71→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 0 38 2095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.78
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.22 41 11.7 %
Rwork0.209 310 -
obs-310 48.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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