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- PDB-4pxi: Elucidation of the Structural and Functional Mechanism of Action ... -

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Basic information

Entry
Database: PDB / ID: 4pxi
TitleElucidation of the Structural and Functional Mechanism of Action of the TetR Family Protein, CprB from S. coelicolor A3(2)
Components
  • CprB
  • DNA (5'-D(*AP*CP*AP*TP*AP*CP*GP*GP*GP*AP*CP*GP*CP*CP*CP*CP*GP*TP*TP*TP*AP*T)-3')
  • DNA (5'-D(*AP*TP*AP*AP*AP*CP*GP*GP*GP*GP*CP*GP*TP*CP*CP*CP*GP*TP*AP*TP*GP*T)-3')
KeywordsTRANSCRIPTION/DNA / CprB-DNA complex / TetR superfamily of transcription regulators / A-factor receptor homolog protein / CprB / Autoregulator / S. coelicolor A3(2) / gamma-butryolactones receptor protein / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily ...: / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / CprB
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHussain, B. / Ruchika, B. / Aruna, B. / Ruchi, A.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2)
Authors: Bhukya, H. / Bhujbalrao, R. / Bitra, A. / Anand, R.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Derived calculations
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CprB
B: CprB
C: CprB
D: CprB
E: DNA (5'-D(*AP*CP*AP*TP*AP*CP*GP*GP*GP*AP*CP*GP*CP*CP*CP*CP*GP*TP*TP*TP*AP*T)-3')
F: DNA (5'-D(*AP*TP*AP*AP*AP*CP*GP*GP*GP*GP*CP*GP*TP*CP*CP*CP*GP*TP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)108,3826
Polymers108,3826
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-87 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.060, 149.060, 69.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT IS TETRAMERIC. ONE IS DIMER PROTEIN (A,B) AND DOUBLE STRANDED DNA (E,F). THE OTHER IS DIMER PROTEIN (C,D) AND DOUBLE STRANDED DNA (E,F).

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Components

#1: Protein
CprB


Mass: 23719.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: cprB / Production host: Escherichia coli (E. coli) / References: UniProt: O66122
#2: DNA chain DNA (5'-D(*AP*CP*AP*TP*AP*CP*GP*GP*GP*AP*CP*GP*CP*CP*CP*CP*GP*TP*TP*TP*AP*T)-3')


Mass: 6712.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized oligonucleotide sequence / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*AP*AP*AP*CP*GP*GP*GP*GP*CP*GP*TP*CP*CP*CP*GP*TP*AP*TP*GP*T)-3')


Mass: 6792.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized oligonucleotide sequence / Source: (synth.) synthetic construct (others)

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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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MgCl2-6H2O, 0.05M Tris-HCl pH7.5, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MAR 225 CCD detector / Detector: CCD / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→129.089 Å / Num. all: 28269 / Num. obs: 28269 / % possible obs: 99.6 % / Redundancy: 3.9 % / Rsym value: 0.128 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.2-3.373.30.5251.50.525198.6
3.37-3.583.20.4191.10.419199.2
3.58-3.823.60.2652.40.265199.8
3.82-4.133.90.1961.90.1961100
4.13-4.534.30.1424.80.1421100
4.53-5.064.30.1056.70.1051100
5.06-5.844.30.09770.0971100
5.84-7.164.30.1036.60.1031100
7.16-10.124.30.0687.80.0681100
10.12-60.9014.20.0915.60.091199.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UI5

1ui5


Resolution: 3.2→60.9 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.884 / SU B: 57.729 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.483 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29433 1163 4.1 %RANDOM
Rwork0.21985 ---
obs0.22299 27073 99.56 %-
all-28269 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.31 Å20 Å2
2---0.63 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 3.2→60.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 856 0 0 6886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0187094
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.8719803
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9475781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28120.958261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.14615985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1241582
X-RAY DIFFRACTIONr_chiral_restr0.1080.21111
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215048
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 92 -
Rwork0.299 2023 -
obs--97.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4828-0.7196-0.97030.2960.25980.34360.1165-0.1135-0.0762-0.0593-0.1124-0.00830.0662-0.0515-0.0040.28140.0217-0.01320.48690.01820.2026-77.925722.0329-14.0487
22.3631-0.49140.30090.3128-0.05650.0483-0.0534-0.1422-0.04570.02770.0802-0.02640.0346-0.0309-0.02680.24420.10880.00520.55260.00510.212-73.974822.057410.8731
31.3247-1.19620.27291.4899-0.24940.06580.13890.0652-0.0483-0.113-0.08860.06370.0454-0.0112-0.05040.37680.1889-0.00960.4091-0.00090.2019-18.4633-10.3261-10.9946
42.4315-1.7519-0.9051.85050.64150.36980.0236-0.1276-0.0504-0.166-0.0160.05570.0497-0.0204-0.00760.40970.1209-0.03290.3682-0.00170.1913-16.4694-13.591213.6242
51.2212-0.63110.49880.3294-0.26260.21140.0503-0.077-0.0151-0.00640.01010.0216-0.0136-0.0275-0.06040.42880.12630.07040.4806-0.0080.1935-40.01916.0187-0.5823
61.1457-0.20690.04110.0452-0.0050.00270.02030.02810.0086-0.02260.0195-0.0221-0.00820.0073-0.03980.39990.13590.01810.5399-0.04640.1869-40.314815.6795-2.3245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 211
2X-RAY DIFFRACTION2B5 - 212
3X-RAY DIFFRACTION3C5 - 212
4X-RAY DIFFRACTION4D8 - 212
5X-RAY DIFFRACTION5E3 - 22
6X-RAY DIFFRACTION6F1 - 22

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