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- PDB-3v78: Crystal Structure of Transcriptional Regulator -

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Basic information

Entry
Database: PDB / ID: 3v78
TitleCrystal Structure of Transcriptional Regulator
ComponentsPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY DEOR-FAMILY)
KeywordsTRANSCRIPTION / helix-turn-helix DNA binding domain
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Tetracyclin repressor-like, C-terminal, group 31 / Tetracyclin repressor-like, C-terminal domain / : / 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 ...Tetracyclin repressor-like, C-terminal, group 31 / Tetracyclin repressor-like, C-terminal domain / : / 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
ETHIDIUM / HTH tetR-type domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsDo, S.V. / Bolla, J.R. / Chen, X. / Yu, E.W.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural and functional analysis of the transcriptional regulator Rv3066 of Mycobacterium tuberculosis.
Authors: Bolla, J.R. / Do, S.V. / Long, F. / Dai, L. / Su, C.C. / Lei, H.T. / Chen, X. / Gerkey, J.E. / Murphy, D.C. / Rajashankar, K.R. / Zhang, Q. / Yu, E.W.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

Deposited unit
A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY DEOR-FAMILY)
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY DEOR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2624
Polymers45,6332
Non-polymers6292
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-19 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.098, 99.098, 66.478
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY DEOR-FAMILY)


Mass: 22816.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3151, Rv3066 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95092
#2: Chemical ChemComp-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris, PEG 4000, MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2011
RadiationMonochromator: scryo-cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 32337 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.383.10.3641100
2.38-2.483.20.261100
2.48-2.593.30.1921100
2.59-2.733.30.1481100
2.73-2.93.30.1091100
2.9-3.123.30.0821100
3.12-3.443.20.072199.9
3.44-3.932.70.061197.4
3.93-4.953.10.045199.4
4.95-403.40.031199.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T6N

3t6n


Resolution: 2.299→39.728 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 0 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 829 5.04 %
Rwork0.2059 --
obs0.2088 16443 96.36 %
all-17079 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.482 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6813 Å20 Å20 Å2
2---0.6813 Å20 Å2
3---1.3625 Å2
Refinement stepCycle: LAST / Resolution: 2.299→39.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 48 64 2763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082746
X-RAY DIFFRACTIONf_angle_d1.0823743
X-RAY DIFFRACTIONf_dihedral_angle_d17.146988
X-RAY DIFFRACTIONf_chiral_restr0.076431
X-RAY DIFFRACTIONf_plane_restr0.004487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2994-2.44350.37091170.24122389X-RAY DIFFRACTION90
2.4435-2.63210.31791710.24452500X-RAY DIFFRACTION95
2.6321-2.89690.29261390.22542609X-RAY DIFFRACTION97
2.8969-3.31590.29781260.22242665X-RAY DIFFRACTION99
3.3159-4.1770.24461570.20192631X-RAY DIFFRACTION97
4.177-39.73370.2181190.18282820X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -35.8108 Å / Origin y: -1.6484 Å / Origin z: 4.8403 Å
111213212223313233
T0.1572 Å20.027 Å20.0549 Å2-0.104 Å20.0045 Å2--0.1697 Å2
L0.1363 °20.4064 °20.0394 °2-0.5633 °2-0.3499 °2--0.9072 °2
S0.0225 Å °-0.0011 Å °0.0408 Å °0.2078 Å °0.0408 Å °0.1585 Å °-0.0733 Å °0.0606 Å °-0.052 Å °
Refinement TLS groupSelection details: all

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