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- PDB-7p6f: 1.93 A resolution X-ray crystal structure of the transcriptional ... -

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Basic information

Entry
Database: PDB / ID: 7p6f
Title1.93 A resolution X-ray crystal structure of the transcriptional regulator SrnR from Streptomyces griseus
ComponentsTranscriptional regulator SrnR
KeywordsDNA BINDING PROTEIN / SrnR / Streptomyces griseus / nickel / transcription factor
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
: / Helix-turn-helix domain / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / Transcriptional regulator SrnR
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMazzei, L. / Ciurli, S.
CitationJournal: Metallomics / Year: 2021
Title: Structure, dynamics, and function of SrnR, a transcription factor for nickel-dependent gene expression.
Authors: Mazzei, L. / Musiani, F. / Zerko, S. / Kozminski, W. / Cianci, M. / Beniamino, Y. / Ciurli, S. / Zambelli, B.
History
DepositionJul 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Transcriptional regulator SrnR
BBB: Transcriptional regulator SrnR
CCC: Transcriptional regulator SrnR
DDD: Transcriptional regulator SrnR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,82211
Polymers50,5174
Non-polymers3057
Water6,251347
1
AAA: Transcriptional regulator SrnR
BBB: Transcriptional regulator SrnR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4827
Polymers25,2592
Non-polymers2235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-32 kcal/mol
Surface area10920 Å2
MethodPISA
2
CCC: Transcriptional regulator SrnR
hetero molecules

CCC: Transcriptional regulator SrnR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3774
Polymers25,2592
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area3490 Å2
ΔGint-19 kcal/mol
Surface area10930 Å2
MethodPISA
3
DDD: Transcriptional regulator SrnR
hetero molecules

DDD: Transcriptional regulator SrnR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3054
Polymers25,2592
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area2860 Å2
ΔGint-32 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.358, 113.358, 124.943
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11CCC-347-

HOH

21DDD-320-

HOH

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Components

#1: Protein
Transcriptional regulator SrnR


Mass: 12629.319 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: srnR / Production host: Escherichia coli (E. coli) / References: UniProt: Q8L1Y3
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 1 uL of SrnR 12.5 mg mL-1 (in 20 mM TrisHCl PH 7.5, 150 mM NaCl, 1 mM TCEP) were added to 20 uL of volatile oil, immediately followed by 1 uL of precipitant containing 0.2 M calcium acetate ...Details: 1 uL of SrnR 12.5 mg mL-1 (in 20 mM TrisHCl PH 7.5, 150 mM NaCl, 1 mM TCEP) were added to 20 uL of volatile oil, immediately followed by 1 uL of precipitant containing 0.2 M calcium acetate hydrate, 0.1 M TrisHCl 8.5, 15 % w/v PEG 4000 (G6 condition of CSSII screening by Molecular Dimensions).
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2019
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.93→124.94 Å / Num. obs: 36223 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.041 / Rrim(I) all: 0.138 / Net I/σ(I): 11.6
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2377 / CC1/2: 0.633 / Rpim(I) all: 0.541 / Rrim(I) all: 1.827 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F6V

3f6v


Resolution: 1.93→51.67 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.335 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2167 1789 4.945 %
Rwork0.178 34392 -
all0.18 --
obs-36181 99.975 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.454 Å20.227 Å20 Å2
2--0.454 Å2-0 Å2
3----1.471 Å2
Refinement stepCycle: LAST / Resolution: 1.93→51.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 19 347 3441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133257
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173219
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.6494409
X-RAY DIFFRACTIONr_angle_other_deg1.451.5777376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.19417.685203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55515563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2721557
X-RAY DIFFRACTIONr_chiral_restr0.090.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023787
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02788
X-RAY DIFFRACTIONr_nbd_refined0.2150.2704
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22908
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21585
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.21468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2570.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.220
X-RAY DIFFRACTIONr_nbd_other0.1970.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.220
X-RAY DIFFRACTIONr_mcbond_it2.4892.7581681
X-RAY DIFFRACTIONr_mcbond_other2.4882.7571680
X-RAY DIFFRACTIONr_mcangle_it3.9374.0862112
X-RAY DIFFRACTIONr_mcangle_other3.9364.0872113
X-RAY DIFFRACTIONr_scbond_it2.8343.1821576
X-RAY DIFFRACTIONr_scbond_other2.8333.1831577
X-RAY DIFFRACTIONr_scangle_it4.5274.6452297
X-RAY DIFFRACTIONr_scangle_other4.5264.6462298
X-RAY DIFFRACTIONr_lrange_it7.49533.8553781
X-RAY DIFFRACTIONr_lrange_other7.46133.1133692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.2761210.2712500X-RAY DIFFRACTION100
1.98-2.0340.2641230.2582429X-RAY DIFFRACTION100
2.034-2.0930.2611280.2392356X-RAY DIFFRACTION100
2.093-2.1580.2691320.2232306X-RAY DIFFRACTION100
2.158-2.2280.2811020.2012241X-RAY DIFFRACTION100
2.228-2.3070.2071190.1772168X-RAY DIFFRACTION100
2.307-2.3940.2411100.1692067X-RAY DIFFRACTION100
2.394-2.4910.235940.1722029X-RAY DIFFRACTION100
2.491-2.6020.2291150.1711933X-RAY DIFFRACTION100
2.602-2.7290.221940.1671866X-RAY DIFFRACTION99.949
2.729-2.8760.246770.1771777X-RAY DIFFRACTION100
2.876-3.0510.244910.1791694X-RAY DIFFRACTION99.944
3.051-3.2610.25790.1831585X-RAY DIFFRACTION100
3.261-3.5220.225860.1731490X-RAY DIFFRACTION100
3.522-3.8580.177760.1661355X-RAY DIFFRACTION99.8604
3.858-4.3120.185510.1411282X-RAY DIFFRACTION100
4.312-4.9780.143660.1381113X-RAY DIFFRACTION100
4.978-6.0930.214570.17952X-RAY DIFFRACTION100
6.093-8.60.2490.169769X-RAY DIFFRACTION100
8.6-51.660.208190.211480X-RAY DIFFRACTION99.0079
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)
11.4917-0.34840.02320.14980.02260.13620.02080.0240.20160.016-0.0785-0.0212-0.00340.04320.05770.0443-0.00570.00010.13680.01260.159421.928829.936368.812
21.2847-0.20740.26130.1866-0.1520.48870.06770.0507-0.084-0.0206-0.0693-0.04250.05260.00070.00160.04580.00080.00190.14930.00820.138334.735912.322969.3792
30.6206-0.2514-0.56830.14940.14590.78120.0143-0.04040.0411-0.01520.03950.01410.08140.0478-0.05390.07760.0097-0.00240.1377-0.00850.11216.327215.427753.7662
41.7614-0.296-0.13280.3548-0.13490.44180.08610.24870.2324-0.02010.0448-0.07420.0077-0.0558-0.13080.02360.0080.04470.20210.06660.174849.614328.324254.0478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA5 - 110
2X-RAY DIFFRACTION2ALLBBB4 - 104
3X-RAY DIFFRACTION3ALLCCC5 - 107
4X-RAY DIFFRACTION4ALLDDD7 - 103

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