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- PDB-4j00: Crystal Structure of Fischerella Transcription Factor HetR comple... -

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Basic information

Entry
Database: PDB / ID: 4j00
TitleCrystal Structure of Fischerella Transcription Factor HetR complexed with 24mer DNA target
Components
  • DNA (5'-D(*TP*GP*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*CP*C)-3')
  • Transcription Factor HetR
KeywordsTranscription/DNA / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helix-turn-helix / DNA-binding domain / transcription factor / Transcription-DNA complex
Function / homology
Function and homology information


heterocyst development / serine-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
HetR, flap domain / HetR, N-terminal DNA-binding domain / Peptidase S48, DNA-binding transcriptional activator HetR / HetR, C-terminal Hood domain / HetR, flap domain / HetR, N-terminal DNA-binding domain / Peptidase family S48 / Heterocyst differentiation regulator C-terminal Hood domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Heterocyst differentiation protein
Similarity search - Component
Biological speciesFischerella thermalis (bacteria)
Anabaena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsKim, Y. / Joachimiak, G. / Gornicki, P. / Joachimiak, A. / MCSG / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets.
Authors: Kim, Y. / Ye, Z. / Joachimiak, G. / Videau, P. / Young, J. / Hurd, K. / Callahan, S.M. / Gornicki, P. / Zhao, J. / Haselkorn, R. / Joachimiak, A.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transcription Factor HetR
B: Transcription Factor HetR
C: DNA (5'-D(*TP*GP*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*CP*C)-3')
D: DNA (5'-D(*TP*GP*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2335
Polymers85,2094
Non-polymers241
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-44 kcal/mol
Surface area50760 Å2
Unit cell
Length a, b, c (Å)92.930, 92.930, 97.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsAs in the asymmetric unit

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Components

#1: Protein Transcription Factor HetR


Mass: 35233.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella thermalis (bacteria) / Strain: PCC 7521 / Gene: hetR / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q2ACK9*PLUS
#2: DNA chain DNA (5'-D(*TP*GP*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*CP*C)-3')


Mass: 7370.752 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the DNA sequence occurs in Anabaena. / Source: (synth.) Anabaena (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % PEG 4000, 50 mM Tris pH 7.5, 160 mM sodium formate, 10 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 18807 / Num. obs: 18807 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 55.5 Å2 / Rsym value: 0.157 / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 905 / Rsym value: 0.709 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IZZ

4izz


Resolution: 3.004→46.465 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.205 965 5.14 %random
Rwork0.168 ---
all0.177 18786 --
obs0.177 18786 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.9 Å2
Refinement stepCycle: LAST / Resolution: 3.004→46.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 978 1 26 5877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036096
X-RAY DIFFRACTIONf_angle_d0.7618439
X-RAY DIFFRACTIONf_dihedral_angle_d19.6062411
X-RAY DIFFRACTIONf_chiral_restr0.049905
X-RAY DIFFRACTIONf_plane_restr0.005923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.0039-3.16220.21831430.20322511265495
3.1622-3.36020.2291510.18422545269694
3.3602-3.61950.22811460.17372551269795
3.6195-3.98330.19941400.16772525266595
3.9833-4.55880.1921470.15772540268795
4.5588-5.74030.18481330.16432556268995
5.7403-37.20770.23441050.18722587269296
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)
12.0001-0.4372-0.64612.28170.02142.2241-0.06340.18580.08990.0377-0.28260.16350.11810.33270.31570.1633-0.0201-0.01530.38170.01410.242424.54637.8278-1.1844
20.9074-0.071-0.64521.2006-0.76911.2217-0.1233-0.02240.0501-0.09970.1133-0.2422-0.23140.35290.15430.4992-0.30130.05170.2656-0.14670.465926.629530.27921.9255
30.3730.24730.41290.8830.48440.6176-0.0107-0.29430.3592-0.072-0.017-0.0707-0.0953-0.2761-0.03170.19640.13150.05780.3380.09440.499525.578311.8615-23.0617
43.5598-1.6809-0.73031.90630.96134.70570.66440.762-0.83320.04890.0827-0.15331.4097-0.2647-0.37610.5410.14-0.10570.7757-0.11880.725134.3183-9.5266-43.3981
50.6220.9498-0.57691.7288-0.15412.33770.0194-0.2215-0.18680.08360.0778-0.26770.27210.1023-0.1090.17680.0296-0.03660.27580.02430.340733.47551.223-26.3106
60.7108-0.54750.3671.2307-0.09461.2777-0.09390.09230.0974-0.227-0.03020.12710.1863-0.22840.17090.17170.01260.03530.3039-0.09730.33981.63061.3006-3.1258
72.0047-0.906-1.73562.26730.21871.55680.03830.03120.1897-0.1470.11880.1984-0.1230.169-0.11110.1397-0.0827-0.07660.460.0130.248926.76389.1857-3.0543
80.9378-0.0492-0.77010.46740.72181.4685-0.0536-0.1468-0.015-0.0760.2209-0.05440.02040.4723-0.04480.2845-0.08070.01030.36720.00460.338628.39819.984319.5181
90.02110.0253-0.09131.99812.55854.13560.2095-0.3291-0.0054-0.0036-0.80260.5336-0.5155-0.45230.26430.2558-0.095-0.03030.38670.01310.592814.473131.788336.4011
102.3076-0.18760.58041.5113-0.05871.38790.0320.0934-0.06020.07970.0327-0.2449-0.20270.1303-0.09950.4497-0.1839-0.07630.4223-0.01520.247525.839921.876422.6395
111.5776-0.6692-0.0940.6420.09570.7302-0.08160.1188-0.60120.1166-0.32980.05220.0475-0.0297-0.00640.0401-0.17320.03010.3521-0.05570.59428.30410.4408-1.969
120.4621-0.42870.64532.6046-0.13891.0270.37610.0543-0.39630.6689-0.31340.5002-0.20080.1682-0.11260.2118-0.07790.00860.38770.08230.4801-4.2996-0.03292.9128
131.901-0.56540.14520.4672-0.35891.71790.33330.7978-0.5488-0.40190.12080.5840.5417-0.1834-0.1950.3656-0.0933-0.27690.52050.1980.469446.4665-10.3134-15.4139
140.76641.0077-0.69651.5415-0.2922.50440.0813-0.18670.28020.3624-0.5264-0.34860.1446-0.49860.17040.15960.0691-0.03880.762-0.01380.627855.67235.6764-7.138
153.5356-0.8777-4.85157.6245-0.91877.5318-0.43530.1599-0.75510.2313-0.1424-1.3031-0.37510.43750.46890.28440.0123-0.00010.3166-0.02450.38543.349921.2134-3.9813
160.0276-0.195-0.20523.99-0.0152.0585-0.2388-1.20560.2131.96190.6239-1.0456-0.58770.9555-0.1860.72050.1259-0.09350.7525-0.18980.554640.575830.485412.2739
172.4597-1.2456-0.27571.17390.19930.0359-0.3704-0.0405-0.3073-0.1529-0.2658-0.57330.08430.2255-0.57272.0305-0.67610.01780.97610.42910.894433.151849.090711.0824
181.9693-1.81342.94971.6696-2.71584.4145-0.0916-0.84230.4806-0.02020.665-0.1119-0.2431-0.4387-0.37050.9029-0.2358-0.06250.703-0.17860.503228.854541.536415.0804
192.7799-0.0091-0.16873.5952.03371.16360.05580.7630.46360.23610.6848-0.73450.51440.7219-0.48610.4402-0.12290.09940.8007-0.15740.494442.517335.9274.5194
200.0093-0.01210.01110.019-0.00230.01590.63960.1334-0.50840.35270.234-0.33690.38540.2586-0.89470.5391-0.1689-0.16810.49380.11990.654545.514216.50781.838
210.10940.0201-0.05050.01520.08440.7599-0.0968-0.3984-0.62420.1324-0.0970.04220.40760.63340.29360.34890.05760.0550.64520.05240.740753.80280.0476-13.9234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 113 )
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 136 )
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 220 )
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 298 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 71 )
8X-RAY DIFFRACTION8chain 'B' and (resid 72 through 123 )
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 151 )
10X-RAY DIFFRACTION10chain 'B' and (resid 152 through 222 )
11X-RAY DIFFRACTION11chain 'B' and (resid 223 through 258 )
12X-RAY DIFFRACTION12chain 'B' and (resid 259 through 298 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 5 )
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 10 )
15X-RAY DIFFRACTION15chain 'C' and (resid 11 through 15 )
16X-RAY DIFFRACTION16chain 'C' and (resid 16 through 20 )
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 24 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 5 )
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 10 )
20X-RAY DIFFRACTION20chain 'D' and (resid 11 through 15 )
21X-RAY DIFFRACTION21chain 'D' and (resid 16 through 24 )

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