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- PDB-7pt0: SCO3201 with putative ligand -

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Basic information

Entry
Database: PDB / ID: 7pt0
TitleSCO3201 with putative ligand
ComponentsTetR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION / REGULATOR / TETR
Function / homologyBacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / SPERMIDINE / TetR family transcriptional regulator
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsWerten, S. / Palm, G.J. / Hinrichs, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Febs J. / Year: 2023
Title: Crystal structures of free and ligand-bound forms of the TetR/AcrR-like regulator SCO3201 from Streptomyces coelicolor suggest a novel allosteric mechanism.
Authors: Werten, S. / Waack, P. / Palm, G.J. / Virolle, M.J. / Hinrichs, W.
#1: Journal: Biochem Biophys Res Commun / Year: 2014
Title: Structure and regulatory targets of SCO3201, a highly promiscuous TetR-like regulator of Streptomyces coelicolor M145.
Authors: Xu, D. / Waack, P. / Zhang, Q. / Werten, S. / Hinrichs, W. / Virolle, M.J.
History
DepositionSep 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4963
Polymers46,3512
Non-polymers1451
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-6 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.128, 79.877, 96.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 26 - 229 / Label seq-ID: 5 - 208

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

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Components

#1: Protein TetR family transcriptional regulator


Mass: 23175.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: gap 119-123 GAGVS, gap 206-208 PQG / Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: HCU77_15975 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6M9XK53
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: analog to PDB entry 4CGR: 40 mg/mL SCO3201 against (0.1 M (NH4)H2PO4, 0.1 M TRIS/HCl pH 5.0)

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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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.89→61.6 Å / Num. obs: 34934 / % possible obs: 99 % / Redundancy: 6.3 % / Biso Wilson estimate: 59.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.04 / Net I/σ(I): 20.7
Reflection shellResolution: 1.89→2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5288 / CC1/2: 0.53 / Rrim(I) all: 1.48 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CGR

4cgr


Resolution: 1.89→48.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / SU B: 10.868 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1727 4.9 %RANDOM
Rwork0.2036 ---
obs0.2043 33204 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.85 Å2 / Biso mean: 64.619 Å2 / Biso min: 40.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å2-0 Å2
2---0.21 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.89→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 10 87 3074
Biso mean--81.43 62.94 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133075
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142946
X-RAY DIFFRACTIONr_angle_refined_deg1.61.6424188
X-RAY DIFFRACTIONr_angle_other_deg1.4211.5696695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.87918.012166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72615444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9621541
X-RAY DIFFRACTIONr_chiral_restr0.0810.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
Refine LS restraints NCS

Ens-ID: 1 / Number: 5363 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.89→1.939 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 141 -
Rwork0.441 2379 -
all-2520 -
obs--99.33 %
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)
11.815-0.29331.72291.2148-0.18492.1186-0.1034-0.1198-0.1427-0.09910.1299-0.3114-0.0925-0.2669-0.02650.25190.0478-0.01590.1345-0.05470.236349.58124.6396.179
20.61671.16391.06512.83041.96514.2541-0.14620.0761-0.0885-0.00880.2171-0.1495-0.01560.4779-0.07090.27290.0319-0.03870.2201-0.09630.162149.09543.75526.432
311.9473-0.7265-0.0232.27522.49062.78120.18690.13380.0179-0.2124-0.0514-0.1072-0.2404-0.0419-0.13550.21260.07410.00530.0994-0.06930.132545.32141.4464.838
40.6563-1.0006-0.51071.81491.42961.8654-0.01650.0656-0.1485-0.035-0.02520.1909-0.1590.11020.04170.3638-0.034-0.10310.1383-0.04070.159138.64344.86523.197
52.0062-6.00758.51818.0844-25.614936.2993-0.0571-0.0243-0.03430.0010.12150.0053-0.0576-0.1988-0.06440.41270.20310.04950.7938-0.29420.377110.18340.794-0.891
62.4961-0.07141.3463.37160.85061.05580.16810.2866-0.21030.198-0.0361-0.0098-0.00270.1023-0.1320.29660.0849-0.09060.0698-0.0490.298213.24430.2478.84
74.02662.54163.28691.60532.07562.6839-0.3187-0.09750.4516-0.1949-0.06080.2966-0.2543-0.08030.37960.3529-0.0029-0.16070.003-0.01480.320221.92451.86515.033
81.7635-0.31712.24410.0766-0.35922.9967-0.635-0.43290.39590.08350.0346-0.02-0.7706-0.70650.60050.5480.0594-0.27620.2931-0.16430.270227.09352.5123.118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 86
2X-RAY DIFFRACTION2A87 - 118
3X-RAY DIFFRACTION3A127 - 139
4X-RAY DIFFRACTION4A140 - 301
5X-RAY DIFFRACTION5B26 - 34
6X-RAY DIFFRACTION6B35 - 86
7X-RAY DIFFRACTION7B87 - 178
8X-RAY DIFFRACTION8B179 - 229

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