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- PDB-4nb5: Crystal Structure of a transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 4nb5
TitleCrystal Structure of a transcriptional regulator
ComponentsDNA binding proteinDNA-binding protein
KeywordsDNA BINDING PROTEIN / DNA binding
Function / homology
Function and homology information


HR1 repeat / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,3-dihydroxypropan-2-yl octadecanoate / HTH-type transcriptional regulator MmpR5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.641 Å
AuthorsSu, C.-C. / Radhakrishnan, A. / Yu, E.W.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of the Transcriptional Regulator Rv0678 of Mycobacterium tuberculosis.
Authors: Radhakrishnan, A. / Kumar, N. / Wright, C.C. / Chou, T.H. / Tringides, M.L. / Bolla, J.R. / Lei, H.T. / Rajashankar, K.R. / Su, C.C. / Purdy, G.E. / Yu, E.W.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA binding protein
B: DNA binding protein
C: DNA binding protein
D: DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5036
Polymers76,7864
Non-polymers7172
Water10,467581
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.539, 57.245, 61.441
Angle α, β, γ (deg.)82.240, 68.400, 72.200
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA binding protein / DNA-binding protein


Mass: 19196.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37rv / Gene: Rv0678, RVBD_0678 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: I6Y8F7
#2: Chemical ChemComp-2JT / 1,3-dihydroxypropan-2-yl octadecanoate / 2-Stearoylglycerol / 2-Monostearin


Mass: 358.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H42O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4
Details: 25% PEG1000, 0.05M NaCl, 0.1M NaAc(4.0), and 4% glycerol, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ACSD / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 78058 / % possible obs: 97 % / Redundancy: 2 % / Rmerge(I) obs: 0.044 / Χ2: 1.001 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.64-1.720.39577181.004195.6
1.7-1.7720.29376891.002195.9
1.77-1.8520.21477421.005196.1
1.85-1.9420.14877611.018196.6
1.94-2.0720.09577801.03196.8
2.07-2.2320.06578161.058197.2
2.23-2.4520.0578591.017197.6
2.45-2.820.04278770.957197.9
2.8-3.531.90.02979090.943198.4
3.53-5020.02179070.972198.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.641→41.165 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8756 / SU ML: 0.16 / σ(F): 1.97 / Phase error: 20.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 3933 5.04 %RANDOM
Rwork0.1662 ---
all0.1674 78052 --
obs0.1674 78052 96.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.26 Å2 / Biso mean: 22.0515 Å2 / Biso min: 4.73 Å2
Refinement stepCycle: LAST / Resolution: 1.641→41.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 50 581 5250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054899
X-RAY DIFFRACTIONf_angle_d0.9026590
X-RAY DIFFRACTIONf_chiral_restr0.052700
X-RAY DIFFRACTIONf_plane_restr0.003880
X-RAY DIFFRACTIONf_dihedral_angle_d15.1621981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6406-1.66060.28881290.23532568269794
1.6606-1.68160.26221330.24112591272496
1.6816-1.70380.26621340.23382624275895
1.7038-1.72710.25461520.21922616276896
1.7271-1.75180.27331460.21482596274296
1.7518-1.77790.24981360.20572637277396
1.7779-1.80570.21981240.20712638276296
1.8057-1.83530.23271350.20232585272096
1.8353-1.8670.25031330.19932655278897
1.867-1.90090.23111160.18782656277297
1.9009-1.93750.22051250.18362680280597
1.9375-1.9770.1971130.17952673278697
1.977-2.020.21051620.1732596275897
2.02-2.0670.20851620.16822628279097
2.067-2.11870.20211480.16292679282797
2.1187-2.1760.16621530.15822637279097
2.176-2.240.2031370.15252633277098
2.24-2.31230.20181550.15192641279697
2.3123-2.39490.19341500.15322660281098
2.3949-2.49080.18141480.15352688283698
2.4908-2.60410.17691490.15242691284098
2.6041-2.74140.15541420.15252655279798
2.7414-2.91310.15631360.16312670280698
2.9131-3.1380.171340.15972708284299
3.138-3.45360.1961550.15562685284099
3.4536-3.9530.161400.14592665280598
3.953-4.9790.15221410.14042715285699
4.979-41.17830.19521450.1882649279497

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