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- PDB-4i6z: Crystal structure of the transcriptional regulator TM1030 with 24... -

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Basic information

Entry
Database: PDB / ID: 4i6z
TitleCrystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide
Components
  • DNA OLIGONUCLEOTIDE
  • Transcriptional regulator, TetR familyTranscriptional regulation
KeywordsTranscription Regulator/DNA / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / PFAM TetR_N / Helix-turn-helix / TRANSCRIPTIONAL REGULATOR / DNA BINDING / Transcription Regulator-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / 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. ...: / Tetracyclin repressor-like, C-terminal domain / 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKoclega, K.D. / Chruszcz, M. / Cooper, D.R. / Petkowski, J.J. / Tkaczuk, K.L. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide
Authors: Koclega, K.D. / Chruszcz, M. / Cooper, D.R. / Petkowski, J.J. / Tkaczuk, K.L. / Joachimiak, A. / Minor, W.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Derived calculations
Revision 1.2May 27, 2015Group: Source and taxonomy
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
C: DNA OLIGONUCLEOTIDE
D: DNA OLIGONUCLEOTIDE


Theoretical massNumber of molelcules
Total (without water)63,5584
Polymers63,5584
Non-polymers00
Water1086
1
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
C: DNA OLIGONUCLEOTIDE
D: DNA OLIGONUCLEOTIDE

A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
C: DNA OLIGONUCLEOTIDE
D: DNA OLIGONUCLEOTIDE


Theoretical massNumber of molelcules
Total (without water)127,1158
Polymers127,1158
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12340 Å2
ΔGint-116 kcal/mol
Surface area43100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.008, 45.954, 82.510
Angle α, β, γ (deg.)90.000, 105.600, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 200 / Label seq-ID: 3 - 202

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Transcriptional regulator, TetR family / Transcriptional regulation


Mass: 24409.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM1030, TM_1030 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: Q9X0C0
#2: DNA chain DNA OLIGONUCLEOTIDE


Mass: 7369.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized DNA / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 310 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 11502 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.095 / Χ2: 2.338 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.264.20.5195741.5521100
3.26-3.314.20.2875721.511100
3.31-3.384.20.2045451.6051100
3.38-3.454.20.1175891.4981100
3.45-3.524.20.2675791.7241100
3.52-3.64.10.2435471.5121100
3.6-3.694.20.25511.4291100
3.69-3.794.20.1815841.5851100
3.79-3.914.10.1595721.5421100
3.91-4.034.20.1265591.6571100
4.03-4.184.20.1065901.6931100
4.18-4.344.20.095571.7751100
4.34-4.544.20.0865831.7471100
4.54-4.784.20.0755612.1291100
4.78-5.084.10.0795902.3651100
5.08-5.474.10.0865692.6721100
5.47-6.024.10.0835872.8111100
6.02-6.894.10.0845843.7821100
6.89-8.674.10.0625864.8481100
8.67-503.80.0536237.467199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ID6

2id6


Resolution: 3.2→33.23 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2524 / WRfactor Rwork: 0.1813 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8025 / SU B: 36.056 / SU ML: 0.391 / SU Rfree: 0.5004 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 549 4.8 %RANDOM
Rwork0.2 ---
obs0.2033 11471 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 221.92 Å2 / Biso mean: 82.3858 Å2 / Biso min: 32.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-1.83 Å2
2---1.13 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 3.2→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 488 0 6 3606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0183718
X-RAY DIFFRACTIONr_bond_other_d0.0040.023205
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.8475127
X-RAY DIFFRACTIONr_angle_other_deg1.07237324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63323.986143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96215481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6841516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023888
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02864
Refine LS restraints NCS

Ens-ID: 1 / Number: 10535 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 36 -
Rwork0.253 805 -
all-841 -
obs--100 %
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)
11.1245-0.75340.13490.5349-0.18131.0597-0.09890.10820.10080.0626-0.0389-0.10160.18-0.17220.13770.0524-0.0362-0.00010.0569-0.02080.099231.3239.2924.283
22.8806-1.2621-0.77960.62540.52310.9409-0.3483-0.267-0.04290.22130.13580.07720.3226-0.02920.21240.151-0.00030.0460.10150.00180.073222.6146.42827.395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 200
2X-RAY DIFFRACTION2B1 - 200

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