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- PDB-4j01: Crystal Structure of Fischerella Transcription Factor HetR comple... -

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Basic information

Entry
Database: PDB / ID: 4j01
TitleCrystal Structure of Fischerella Transcription Factor HetR complexed with 29mer DNA target
Components
  • DNA (29-MER)
  • 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: 3.246 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 (29-MER)
D: DNA (29-MER)
E: Transcription Factor HetR
F: Transcription Factor HetR
G: DNA (29-MER)
H: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,6859
Polymers176,5898
Non-polymers961
Water1448
1
A: Transcription Factor HetR
B: Transcription Factor HetR
C: DNA (29-MER)
D: DNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)88,2944
Polymers88,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19360 Å2
ΔGint-143 kcal/mol
Surface area40010 Å2
MethodPISA
2
E: Transcription Factor HetR
F: Transcription Factor HetR
G: DNA (29-MER)
H: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3915
Polymers88,2944
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20080 Å2
ΔGint-181 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.157, 182.182, 78.366
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAs in the asymmetric unit

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Components

#1: Protein
Transcription Factor HetR


Mass: 35233.547 Da / Num. of mol.: 4
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 (29-MER)


Mass: 8913.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: the DNA sequence occurs in Anabaena / Source: (synth.) Anabaena (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % PEG 2000MME, 100 mM Hepes pH 7.5, 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: 0.91948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91948 Å / Relative weight: 1
ReflectionResolution: 3.246→50 Å / Num. all: 33964 / Num. obs: 33964 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 79.4 Å2 / Rsym value: 0.134 / Net I/σ(I): 5.5
Reflection shellResolution: 3.246→3.31 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1542 / Rsym value: 0.779 / % possible all: 91.7

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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: 3.246→35.904 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1739 5.15 %random
Rwork0.241 ---
all0.235 33750 --
obs0.235 33750 97.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 138.3 Å2
Refinement stepCycle: LAST / Resolution: 3.246→35.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9656 2364 5 8 12033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412544
X-RAY DIFFRACTIONf_angle_d0.83317438
X-RAY DIFFRACTIONf_dihedral_angle_d20.5554980
X-RAY DIFFRACTIONf_chiral_restr0.051876
X-RAY DIFFRACTIONf_plane_restr0.0041840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.2461-3.34160.36581300.3242381251183
3.3416-3.44930.33821390.31712602274190
3.4493-3.57250.35271260.31732681280793
3.5725-3.71540.32361610.31222712287394
3.7154-3.88430.30231390.30312716285595
3.8843-4.08880.33971430.29012721286495
4.0888-4.34460.2921350.26612752288795
4.3446-4.67940.27161400.24882682282294
4.6794-5.14910.28281490.23882703285294
5.1491-5.89130.26091400.22522730287094
5.8913-7.41170.27431490.22992690283993
7.4117-35.90660.20811560.142672282891
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)
12.82180.0725-0.39483.31130.76041.2642-0.3553-0.14020.2603-0.7926-0.11420.46820.1735-0.1215-01.3821-0.1321-0.09121.22710.05370.67727.0185.36039.5682
20.1648-0.14440.12610.274-0.38651.0106-0.30590.47950.2979-0.37870.7970.0393-0.4632-0.305901.8281-0.21770.06631.39010.07451.24522.9371-1.9567-0.4414
31.3852-0.2851-0.33690.3924-0.18930.2622-0.2495-0.5151-0.29810.8613-0.0018-0.2191-1.10912.3702.1405-0.31770.09991.42920.00711.930228.247-15.91139.5421
41.5467-0.46231.19662.3085-0.83862.0525-0.66220.33851.1102-1.05390.2872-0.16141.4899-0.28013.2031.683-0.20770.30992.3572-0.8227-0.661930.070712.996426.8937
50.3284-0.47630.08131.8760.15140.98660.18660.7298-1.23980.5119-0.80240.32230.3650.0919-0.03272.0361-0.21320.11041.8974-0.15990.983833.014312.396242.3399
60.99960.41690.84881.91780.06380.9527-0.2568-0.34090.069-0.66670.09780.236-0.0573-0.0236-01.3661-0.0568-0.06741.1333-0.03760.977144.085419.527211.5692
72.7918-0.12830.95610.9514-1.3642.49320.25420.0951-0.1408-1.49490.0317-1.289-0.84130.02240.00341.7926-0.20070.06491.2096-0.06091.121351.179544.25689.1371
81.92980.9373-0.26020.74820.82981.6920.2779-0.5558-0.02090.2981-0.4687-0.22820.0777-0.2637-01.53310.0765-0.17181.6826-0.17390.573337.705723.651432.9843
90.19790.0262-0.06890.04280.03820.16330.77830.7839-0.4993-0.5892-1.03810.1273-0.4157-0.849302.7095-0.17790.51461.192-0.25562.189541.8389-20.9956-7.4282
100.4310.10920.509-0.00780.02740.3261-0.562-0.6554-0.1923-1.14470.02740.9646-0.88040.838101.9063-0.08330.06431.2282-0.15441.341846.8358-3.8976-9.478
112.0014-2.3728-0.17291.92320.15170.0733-0.15921.82740.158-1.52010.28620.0556-1.1577-0.1395-0.72593.2509-0.5807-0.2631.01580.15381.212835.477710.7949-13.7229
120.247-0.19490.05770.1158-0.07160.3239-0.0665-0.29191.37860.98670.0520.0582-0.997-0.1134-02.0974-0.2298-0.28531.0404-0.11181.103839.229427.0072-4.576
131.0692-0.05640.0359-0.0268-0.0172-0.0304-0.18450.55181.99040.22930.8706-0.37050.1527-0.4267-02.7107-0.36190.02431.15250.28242.342930.379949.5211-4.0155
140.3177-0.0244-0.37690.00080.08890.15170.13031.70072.044-1.05181.02780.55381.0351-0.51970.02062.6502-0.1165-0.65051.64040.34981.61131.659246.821-3.8275
150.40130.234-0.38440.1663-0.16450.4529-0.4631-0.54040.6146-1.55560.0980.25291.66140.011302.6361-0.48730.03841.1526-0.29871.840940.473724.515-11.7318
160.12790.0476-0.01480.0303-0.00930.1050.9392-0.3656-0.7522-1.3486-0.55820.7251-0.132-0.1585-01.4162-0.1099-0.21871.0535-0.04062.197835.85557.3027-6.0283
170.03310.05290.08790.05940.10010.2121-0.83611.3611-0.2184-0.78030.39950.30040.10770.5639-02.3597-0.3171-0.16531.3164-0.52731.76144.0073-9.5641-14.6029
180.01210.0193-0.01450.0331-0.04080.0821.3254-1.4082-0.09060.2936-1.5084-0.64281.0061.319502.25690.23230.02481.3111-0.09111.885847.4356-20.4194-1.6269
194.6326-0.21690.05144.4043-0.95593.24210.16340.3324-0.156-0.51590.01070.31220.09240.2311-00.59730.1203-0.17891.0237-0.11160.93019.1582-35.082432.1078
200.09050.18770.22070.18990.32250.53130.90711.04332.21040.4484-0.21250.3039-1.08950.5072-0.00021.60430.12580.34921.8930.56231.89789.444-1.460717.14
210.03450.0144-0.1350.2395-0.22510.31750.95740.73490.6015-0.873-0.2293-0.9964-1.85291.357401.8877-0.14590.46041.6298-0.15552.47968.335711.575324.3641
220.955-0.50270.32420.8259-0.12150.13060.15371.2211-0.1705-0.13550.05880.50490.839-0.351101.1967-0.1907-0.06721.60770.1471.3586-0.4093-12.63622.2801
231.73352.92641.43175.3371.19733.91622.66620.12410.0803-0.08291.87310.4076-0.51880.86628.33040.462-1.55421.169-0.01090.95963.0169.56260.351829.164
240.9323-1.0263-0.24343.381-2.23760.95670.20270.2688-0.35860.262-0.7851-0.22310.50090.788-00.90830.00810.03541.77440.13161.471336.6385-28.286333.0543
253.55850.0944-0.17817.2299-1.65542.9788-0.22360.48840.16430.7759-0.27680.67680.00140.2011-0.00560.50190.02010.18571.2017-0.01180.60658.9682-27.37440.8924
261.15020.46610.20180.5616-0.40121.03040.0182-0.10451.60461.47370.0008-0.19110.80180.4615-01.52470.0831-0.24941.2093-0.08450.47214.4875-67.28354.4384
270.74870.7867-0.61961.6229-0.35561.6010.0218-0.15090.66330.41410.32870.462-0.83970.095201.1948-0.0511-0.06881.1761-0.00521.25187.4128-54.084750.2592
280.8661-0.45750.7430.47830.28861.7776-0.5273-0.912-0.6188-2.6132-1.15460.44420.0940.415601.18110.1773-0.20861.18950.0471.424114.208-63.345144.7739
291.1578-2.3738-0.89298.02952.48080.69240.23570.53660.3638-0.7820.0679-2.46-0.3614-0.69510.77320.6682-0.2754-0.25431.98670.28021.272832.6608-28.449535.4127
300.7608-1.59120.56642.1055-0.83790.24180.88750.91760.4401-0.5909-0.8202-1.9612-0.23181.2707-0.00530.9327-0.1107-0.03281.95860.48221.946443.5508-31.323338.8309
310.0292-0.00060.06480.067-0.10540.1758-0.28291.1443-0.4105-0.20470.5817-0.0433-0.988-0.4506-02.4802-0.147-0.11621.5973-0.2762.8929-8.19825.807541.7927
320.6024-0.41-0.37550.3732-0.1210.69950.5289-0.60420.18710.2149-0.01990.42250.2075-0.9318-01.1923-0.07740.18081.4617-0.1191.9027-12.2991-18.520240.8708
330.0753-0.2501-0.27160.99740.89450.81191.35890.753-0.3487-1.9349-0.3028-0.65080.3704-0.69010.01610.8910.12170.01841.67820.15692.2905-5.0584-42.239738.7364
34-0.0060.0283-0.04970.00280.20490.32430.1207-0.72680.0134-0.90751.3311.25621.25881.362801.8762-0.2098-0.35242.0699-0.28722.5993-4.825-64.525429.4211
350.00630.01660.0585-0.00510.02830.2310.8111-0.46940.55360.59091.49660.56550.98540.8525-02.5062-0.0183-0.64451.3132-0.12153.2216-2.3843-69.89834.982
360.18010.0555-0.1580.0444-0.02470.05370.65970.75511.24070.02551.50961.28660.7204-0.23901.7792-0.0359-0.43951.39590.28842.1523-7.2414-54.06628.0207
370.51410.2583-0.06570.1531-0.21830.2583-0.1752-0.61990.40760.011-0.15782.58840.3884-0.9937-0.00041.3623-0.0528-0.17831.3940.11711.8764-10.1594-31.466237.989
380.3467-0.3184-0.16040.52650.07190.2633-0.30090.1187-0.32942.00950.2547-0.2471-1.1492-0.41880.00292.14240.21040.02631.16140.24512.5087-9.6374-1.120145.713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 192 )
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 220 )
4X-RAY DIFFRACTION4chain 'A' and (resid 221 through 242 )
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 298 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 123 )
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 193 )
8X-RAY DIFFRACTION8chain 'B' and (resid 194 through 298 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 5 )
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 10 )
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 15 )
12X-RAY DIFFRACTION12chain 'C' and (resid 16 through 20 )
13X-RAY DIFFRACTION13chain 'C' and (resid 21 through 29 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 10 )
15X-RAY DIFFRACTION15chain 'D' and (resid 11 through 15 )
16X-RAY DIFFRACTION16chain 'D' and (resid 16 through 20 )
17X-RAY DIFFRACTION17chain 'D' and (resid 21 through 25 )
18X-RAY DIFFRACTION18chain 'D' and (resid 26 through 29 )
19X-RAY DIFFRACTION19chain 'E' and (resid 5 through 100 )
20X-RAY DIFFRACTION20chain 'E' and (resid 101 through 123 )
21X-RAY DIFFRACTION21chain 'E' and (resid 124 through 151 )
22X-RAY DIFFRACTION22chain 'E' and (resid 152 through 192 )
23X-RAY DIFFRACTION23chain 'E' and (resid 193 through 220 )
24X-RAY DIFFRACTION24chain 'E' and (resid 221 through 298 )
25X-RAY DIFFRACTION25chain 'F' and (resid 5 through 100 )
26X-RAY DIFFRACTION26chain 'F' and (resid 101 through 138 )
27X-RAY DIFFRACTION27chain 'F' and (resid 139 through 192 )
28X-RAY DIFFRACTION28chain 'F' and (resid 193 through 220 )
29X-RAY DIFFRACTION29chain 'F' and (resid 221 through 262 )
30X-RAY DIFFRACTION30chain 'F' and (resid 263 through 298 )
31X-RAY DIFFRACTION31chain 'G' and (resid 1 through 5 )
32X-RAY DIFFRACTION32chain 'G' and (resid 6 through 15 )
33X-RAY DIFFRACTION33chain 'G' and (resid 16 through 20 )
34X-RAY DIFFRACTION34chain 'G' and (resid 21 through 29 )
35X-RAY DIFFRACTION35chain 'H' and (resid 1 through 5 )
36X-RAY DIFFRACTION36chain 'H' and (resid 6 through 10 )
37X-RAY DIFFRACTION37chain 'H' and (resid 11 through 20 )
38X-RAY DIFFRACTION38chain 'H' and (resid 21 through 29 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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