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- PDB-3b6a: Crystal structure of the Streptomyces coelicolor TetR family prot... -

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Basic information

Entry
Database: PDB / ID: 3b6a
TitleCrystal structure of the Streptomyces coelicolor TetR family protein ActR in complex with actinorhodin
ComponentsActR protein
KeywordsTRANSCRIPTION / transcriptional repressor / DNA-binding protein / TetR family / actinorhodin / ligand / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ZCT / ActII protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsWillems, A.R. / Junop, M.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA.
Authors: Willems, A.R. / Tahlan, K. / Taguchi, T. / Zhang, K. / Lee, Z.Z. / Ichinose, K. / Junop, M.S. / Nodwell, J.R.
History
DepositionOct 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: ActR protein
B: ActR protein
C: ActR protein
D: ActR protein
E: ActR protein
F: ActR protein
G: ActR protein
H: ActR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,68116
Polymers201,6048
Non-polymers5,0768
Water00
1
A: ActR protein
B: ActR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6704
Polymers50,4012
Non-polymers1,2692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
MethodPISA
2
C: ActR protein
D: ActR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6704
Polymers50,4012
Non-polymers1,2692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
MethodPISA
3
E: ActR protein
F: ActR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6704
Polymers50,4012
Non-polymers1,2692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
MethodPISA
4
G: ActR protein
H: ActR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6704
Polymers50,4012
Non-polymers1,2692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.880, 79.000, 107.190
Angle α, β, γ (deg.)89.56, 89.92, 89.88
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALAAA28 - 2453 - 220
21METMETALAALACC28 - 2453 - 220
31METMETALAALAEE28 - 2453 - 220
41METMETALAALAGG28 - 2453 - 220
12ALAALAGLUGLUBB29 - 2434 - 218
22ALAALAGLUGLUDD29 - 2434 - 218
32ALAALAGLUGLUFF29 - 2434 - 218
42ALAALAGLUGLUHH29 - 2434 - 218

NCS ensembles :
ID
1
2

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Components

#1: Protein
ActR protein / Putative transcriptional regulatory protein


Mass: 25200.555 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: M145 / Gene: actR / Plasmid: pPROEX-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53901
#2: Chemical
ChemComp-ZCT / 2,2'-[(1R,1'R,3S,3'S)-6,6',9,9'-tetrahydroxy-1,1'-dimethyl-5,5',10,10'-tetraoxo-3,3',4,4',5,5',10,10'-octahydro-1H,1'H-8,8'-bibenzo[g]isochromene-3,3'-diyl]diacetic acid


Mass: 634.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C32H26O14 / Comment: antibiotic*YM
Nonpolymer detailsTHE CA INDEX NUMBER OF COMPOUND ZCT IS 1397-77-9.

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG4000, 100 mM sodium acetate, 40 mM Tris, 25 mM KCl, 0.5 mM DTT, 15 mg/mL protein, 0.3 uL of 17 mM actinorhodin, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2006 / Details: collimating and focusing mirrors
RadiationMonochromator: Si(111)2 crystals (not channel-cut) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.05→37.12 Å / Num. obs: 34551 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.88 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.6
Reflection shellResolution: 3.05→3.129 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
d*TREKdata reduction
d*TREKdata scaling
CCP46.0.0phasing
Coot0.1.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OPT

2opt


Resolution: 3.05→37.12 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.888 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.623 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28835 939 3.1 %RANDOM
Rwork0.25988 ---
obs0.26077 29797 85.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.765 Å2
Baniso -1Baniso -2Baniso -3
1--3.88 Å20.18 Å2-0.08 Å2
2--7.5 Å20.21 Å2
3----3.63 Å2
Refinement stepCycle: LAST / Resolution: 3.05→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12788 0 400 0 13188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113392
X-RAY DIFFRACTIONr_bond_other_d0.0030.0232
X-RAY DIFFRACTIONr_angle_refined_deg1.5522.02318228
X-RAY DIFFRACTIONr_angle_other_deg1.24396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12951672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2123.194576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.368152172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.83215132
X-RAY DIFFRACTIONr_chiral_restr0.0930.22076
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210148
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.26331
X-RAY DIFFRACTIONr_nbd_other0.3280.263
X-RAY DIFFRACTIONr_nbtor_refined0.3050.29113
X-RAY DIFFRACTIONr_nbtor_other0.120.24
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3381.58340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.619213256
X-RAY DIFFRACTIONr_scbond_it0.85435052
X-RAY DIFFRACTIONr_scangle_it1.4044.54972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1616tight positional0.030.05
12C1616tight positional0.030.05
13E1616tight positional0.030.05
14G1616tight positional0.030.05
21B1581tight positional0.020.05
22D1581tight positional0.030.05
23F1581tight positional0.030.05
24H1581tight positional0.030.05
11A1616tight thermal0.050.5
12C1616tight thermal0.050.5
13E1616tight thermal0.050.5
14G1616tight thermal0.050.5
21B1581tight thermal0.040.5
22D1581tight thermal0.050.5
23F1581tight thermal0.050.5
24H1581tight thermal0.050.5
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 71 -
Rwork0.35 2451 -
obs--96.85 %
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)
12.2656-0.0067-2.37630.0977-0.42844.4339-0.06550.25310.0134-0.0801-0.08660.03640.1823-0.23110.15210.17960.0797-0.0207-0.1911-0.020.197920.547-10.568-47.682
41.0811-0.40990.97810.7213-1.04334.0305-0.0885-0.37820.01440.0868-0.0630.1448-0.3311-0.30510.15150.07310.00920.0599-0.0016-0.03830.188922.8544.95-59.425
52.05040.20242.28070.0210.26083.8318-0.08360.2218-0.0103-0.0805-0.0840.0014-0.17980.21040.16760.21190.08970.0159-0.1738-0.05130.16561.3647.5235.902
21.1577-0.3947-1.03310.6670.69684.1782-0.0805-0.4695-0.14180.0767-0.0971-0.08680.28870.38050.17760.06820.0057-0.02820.05850.0230.1632-0.951-8.128-5.819
31.9427-0.1252.14040.0711-0.46454.0522-0.0533-0.2751-0.05170.1054-0.08540.0273-0.2071-0.22450.13870.1962-0.00160.0345-0.1383-0.01810.1626-8.389-32.291-39.662
61.31280.4363-1.260.871-0.71543.8952-0.10380.3936-0.1023-0.0338-0.06110.0590.2143-0.36230.16480.07640.0854-0.05530.0223-0.03230.1621-6.126-47.729-27.891
72.27520.0496-1.91820.03310.20463.5161-0.0677-0.1597-0.02630.0918-0.06910.0150.18460.27330.13690.2052-0.0153-0.0016-0.1181-0.04440.1604-27.40829.38713.945
81.05330.61261.48751.15720.8493.8537-0.12680.38280.1602-0.0753-0.1009-0.0248-0.20710.40680.22770.06310.10530.06690.02680.00140.1419-29.71445.01425.765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 2453 - 220
2X-RAY DIFFRACTION4BB29 - 2434 - 218
3X-RAY DIFFRACTION5CC28 - 2453 - 220
4X-RAY DIFFRACTION2DD29 - 2434 - 218
5X-RAY DIFFRACTION3EE28 - 2453 - 220
6X-RAY DIFFRACTION6FF29 - 2434 - 218
7X-RAY DIFFRACTION7GG28 - 2453 - 220
8X-RAY DIFFRACTION8HH29 - 2434 - 218

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