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- PDB-7zpn: Crystal Structure of IscR from Dinoroseobacter shibae -

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Basic information

Entry
Database: PDB / ID: 7zpn
TitleCrystal Structure of IscR from Dinoroseobacter shibae
ComponentsHTH-type transcriptional regulator
KeywordsGENE REGULATION / transcription regulator / iron dependent regulator / DNA binding
Function / homology
Function and homology information


DNA-binding transcription factor activity / cytosol
Similarity search - Function
Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator
Similarity search - Component
Biological speciesDinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLukat, P. / Ploetzky, L. / Blankenfeldt, W. / Jahn, D. / Haertig, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dinoroseobacter shibae IscR homolog acts as a repressor for iron acquisition genes
Authors: Ploetzky, L. / Maass, H. / Behringer, M. / Lukat, P. / Blankenfeldt, W. / Jahn, D. / Haertig, E.
History
DepositionApr 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator
B: HTH-type transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,23110
Polymers39,4672
Non-polymers7658
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-109 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.971, 70.971, 149.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

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Components

#1: Protein HTH-type transcriptional regulator


Mass: 19733.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HTH-type transcriptional regulator IscR from Dinoroseobacter shibae containing N-terminal Strep-tag II and PreScission protease cleavage site (not cleaved)
Source: (gene. exp.) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Strain: DSM 16493 / NCIMB 14021 / DFL 12 / Gene: iscR, Dshi_1633 / Plasmid: pET52bStrepII / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21CD+(DE3)RIL / References: UniProt: A8LL11
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 30 % (v/v) PEG 200 100 mM CAPS/ NaOH pH 10,5 200 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.94→56.87 Å / Num. obs: 33461 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 43.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.012 / Rrim(I) all: 0.052 / Net I/σ(I): 29.7 / Num. measured all: 656968
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 20 % / Rmerge(I) obs: 1.053 / Num. measured all: 95731 / Num. unique obs: 4798 / CC1/2: 0.871 / Rpim(I) all: 0.241 / Rrim(I) all: 1.081 / Net I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
autoPROC1.0.5 (20190301)data processing
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CIC

4cic


Resolution: 1.94→56.87 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1706 5.11 %
Rwork0.194 31704 -
obs0.195 33410 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.86 Å2 / Biso mean: 59.26 Å2 / Biso min: 30.13 Å2
Refinement stepCycle: final / Resolution: 1.94→56.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 48 97 2115
Biso mean--82.97 54.78 -
Num. residues----256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.94-1.990.33281550.311725622717
1.99-2.060.2771330.267426072740
2.06-2.130.24681330.212326262759
2.13-2.220.20941370.187326112748
2.22-2.320.20621410.196926122753
2.32-2.440.23241600.200325922752
2.44-2.590.25861330.234326202753
2.59-2.790.27531310.198826422773
2.79-3.070.2371390.212226622801
3.07-3.520.22071420.197826582800
3.52-4.430.19091700.161826732843
4.43-56.870.20461320.1928392971
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)
10.19780.14960.0690.24480.07150.0928-0.02990.5832-0.61730.0086-0.283-0.52130.46331.0865-0.00020.9113-0.076-0.04591.04360.03920.740621.677421.450359.607
23.04410.2377-0.05291.4316-0.10341.9031-0.06671.2481.1047-0.42760.22180.4511-0.8164-0.42190.02780.4299-0.1335-0.01380.41380.01650.3757.87514.961657.1512
30.0949-0.08550.07020.0788-0.0630.05170.19-0.39870.48172.0614-0.29970.72930.1706-1.1168-0.01080.9145-0.22480.13240.7367-0.0820.4408-3.24354.895560.0473
40.3157-0.3776-0.01440.5330.09990.2674-0.2970.29860.2158-0.6020.15071.0541-0.3927-0.8543-0.00030.4758-0.1126-0.07580.6350.04120.56731.089811.932149.9229
50.1393-0.0420.22390.40760.20610.52430.00720.8086-0.09-0.5567-0.1342-0.39320.04160.8788-0.00090.4152-0.1279-0.01120.5194-0.01350.397412.34795.819352.7393
61.9275-0.7561-0.31481.04930.57310.43650.2847-0.253-0.31620.536-0.2863-0.23090.6773-0.30740.00020.5459-0.2125-0.00970.39370.00060.29366.19813.175762.5255
70.70090.4133-0.50241.12580.35180.83470.1429-0.29220.11870.1848-0.23410.22890.04550.2449-0.00030.3969-0.1213-0.02560.4087-0.0320.40514.458714.111861.1991
80.67310.77450.1330.81070.13940.4726-0.13810.04820.6993-0.2984-0.01280.8118-0.3026-0.10880.00010.4565-0.0924-0.03010.3797-0.02410.540211.231828.58464.0318
92.26980.7758-1.0721.6833-0.37960.5073-0.1014-1.1666-0.85861.2373-0.1941-0.3376-0.05370.5651-0.020.6529-0.202-0.05320.58620.10010.423431.192537.501574.3276
100.34030.33060.05990.34020.00160.13920.12871.2310.0209-0.5378-0.1731-0.0142-0.0282-0.13070.00040.9888-0.0374-0.02260.895-0.10410.827422.91830.441158.3186
111.8568-0.4632-0.3221.1470.1290.9411-0.10070.5952-0.8661-0.06290.2858-0.78820.62721.10530.01770.415-0.09540.02150.42730.00420.493635.968636.882362.1371
120.66970.1927-0.26511.4458-0.98070.90570.0967-0.2328-0.24080.66690.0181-1.0074-0.06890.87860.0020.5104-0.14190.04630.63820.01130.668845.442642.724562.4136
132.38151.33680.29692.957-0.28473.2454-0.08390.22510.0672-0.40030.04960.0576-0.38740.2017-0.00810.4761-0.16560.00150.39440.02870.36434.250345.909959.5185
140.2812-0.002-0.49991.67680.2941.39090.1556-0.0621-0.62730.0988-0.2299-0.81070.15560.2752-0.00010.4685-0.1548-0.06460.40880.1020.465427.274426.374769.8767
150.42930.24110.09990.25370.20810.4218-0.3564-0.32660.2760.46570.04820.7876-0.5901-0.4090.00020.5592-0.06830.00190.4462-0.02240.46774.747719.356968.9285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -7 THROUGH 4 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 5 THROUGH 19 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 20 THROUGH 27 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 28 THROUGH 38 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 39 THROUGH 51 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 52 THROUGH 75 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 76 THROUGH 103 )A0
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 104 THROUGH 126 )A0
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 127 THROUGH 137 )A0
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID -7 THROUGH 4 )B0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 5 THROUGH 19 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 20 THROUGH 38 )B0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 39 THROUGH 103 )B0
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 104 THROUGH 126 )B0
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 127 THROUGH 137 )B0

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