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- PDB-3zql: DNA-bound form of TetR-like repressor SimR -

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Basic information

Entry
Database: PDB / ID: 3zql
TitleDNA-bound form of TetR-like repressor SimR
Components
  • 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
  • 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
  • PUTATIVE REPRESSOR SIMREG2
KeywordsPROTEIN-DNA COMPLEX / ANTIBIOTIC RESISTANCE / TETR-LIKE PROTEINS / TRANSCRIPTIONAL REGULATION / STREPTOMYCES
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / metal ion binding
Similarity search - Function
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 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
DNA / DNA (> 10) / Putative repressor SimReg2
Similarity search - Component
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLe, T.B.K. / Schumacher, M.A. / Lawson, D.M. / Brennan, R.G. / Buttner, M.J.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The Crystal Structure of the Tetr Family Transcriptional Repressor Simr Bound to DNA and the Role of a Flexible N-Terminal Extension in Minor Groove Binding.
Authors: Le, T.B.K. / Schumacher, M.A. / Lawson, D.M. / Brennan, R.G. / Buttner, M.J.
History
DepositionJun 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PUTATIVE REPRESSOR SIMREG2
B: PUTATIVE REPRESSOR SIMREG2
C: PUTATIVE REPRESSOR SIMREG2
D: PUTATIVE REPRESSOR SIMREG2
E: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
F: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
G: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
H: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)141,7908
Polymers141,7908
Non-polymers00
Water00
1
C: PUTATIVE REPRESSOR SIMREG2
D: PUTATIVE REPRESSOR SIMREG2
G: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
H: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)70,8954
Polymers70,8954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-71.3 kcal/mol
Surface area26020 Å2
MethodPISA
2
A: PUTATIVE REPRESSOR SIMREG2
B: PUTATIVE REPRESSOR SIMREG2
E: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
F: 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)70,8954
Polymers70,8954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-69.9 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.788, 112.613, 163.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEUAA7 - 2417 - 241
21VALVALLEULEUBB7 - 2417 - 241
12VALVALASPASPAA7 - 2427 - 242
22VALVALASPASPCC7 - 2427 - 242
13VALVALLEULEUAA7 - 2417 - 241
23VALVALLEULEUDD7 - 2417 - 241
14VALVALLEULEUBB7 - 2417 - 241
24VALVALLEULEUCC7 - 2417 - 241
15VALVALASPASPBB7 - 2427 - 242
25VALVALASPASPDD7 - 2427 - 242
16VALVALLEULEUCC7 - 2417 - 241
26VALVALLEULEUDD7 - 2417 - 241
17DTDTDADAEE1 - 171 - 17
27DTDTDADAFF1 - 171 - 17
18DTDTDADAEE1 - 171 - 17
28DTDTDADAGG1 - 171 - 17
19DTDTDADAEE1 - 171 - 17
29DTDTDADAHH1 - 171 - 17
110DTDTDADAFF1 - 171 - 17
210DTDTDADAGG1 - 171 - 17
111DTDTDADAFF1 - 171 - 17
211DTDTDADAHH1 - 171 - 17
112DTDTDADAGG1 - 171 - 17
212DTDTDADAHH1 - 171 - 17

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
PUTATIVE REPRESSOR SIMREG2 / SIMR / SIM16


Mass: 30240.215 Da / Num. of mol.: 4 / Fragment: RESIDUES 3-216
Source method: isolated from a genetically manipulated source
Details: SIMR HAS BEEN REFERRED TO BY TWO ALTERNATIVE NAMES ELSEWHERE. (1) SIMREG2 IN TREFZER ET AL. (2002) ANTIMICROB AGENTS CHEMOTHER, 46,1174-1182. (2) SIM16 IN GALM ET AL. (2002) ARCH MICROBIOL, 178,102-114.
Source: (gene. exp.) STREPTOMYCES ANTIBIOTICUS (bacteria) / Strain: TU 6040 / Plasmid: PIJ10499 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9AMH9
#2: DNA chain 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3'


Mass: 5187.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) STREPTOMYCES ANTIBIOTICUS (bacteria)
#3: DNA chain 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3'


Mass: 5227.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) STREPTOMYCES ANTIBIOTICUS (bacteria)
Sequence detailsBEGINS AT RESIDUE 3 OF DATABASE ENTRY.

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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: 2.79 Å3/Da / Density % sol: 62.5 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT 200 MICROMOLAR AND DNA AT 200 MICROMOLAR WERE MIXED WITH 10% PEG 8000, 0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE IN 0.05 M SODIUM CACODYLATE PH6.5 IN A 1:1 RATIO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.99→92.78 Å / Num. obs: 31030 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 8.3
Reflection shellResolution: 2.99→3.15 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.8 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y2Z

2y2z


Resolution: 2.99→92.78 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 40.223 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.25103 1576 5.1 %RANDOM
Rwork0.20954 ---
obs0.21159 29372 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å20 Å2
2---6.67 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.99→92.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7161 1382 0 0 8543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028882
X-RAY DIFFRACTIONr_bond_other_d0.0040.025585
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.91112383
X-RAY DIFFRACTIONr_angle_other_deg1.093313442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5935918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97322.939330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.183151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.941569
X-RAY DIFFRACTIONr_chiral_restr0.060.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219079
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021888
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A79310.03
12B79310.03
21A81860.02
22C81860.02
31A78680.03
32D78680.03
41B79220.04
42C79220.04
51B79310.03
52D79310.03
61C78610.04
62D78610.04
71E10970.1
72F10970.1
81E11490.01
82G11490.01
91E10990.09
92H10990.09
101F10970.1
102G10970.1
111F11360.05
112H11360.05
121G11000.1
122H11000.1
LS refinement shellResolution: 2.99→3.068 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 115 -
Rwork0.373 2015 -
obs--95.13 %
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)
13.48943.92461.35425.0382.92383.7257-0.16930.3083-0.0768-0.40770.2048-0.0922-0.3777-0.1461-0.03540.62170.1006-0.17280.45670.11620.37353.7404-30.20818.1973
21.2220.87292.11230.84131.48835.596-0.0971-0.03140.0774-0.13210.0126-0.19550.35750.50130.08440.27470.1055-0.00830.331-0.02520.32512.8607-13.73616.9717
33.32681.03591.14081.71911.01340.7038-0.0986-0.32190.09650.15260.163-0.06660.08220.042-0.06430.43130.1130.00790.50710.02560.24957.0781-14.446335.7497
41.06250.4149-0.83764.0815-1.81922.18630.1601-0.20540.2180.1523-0.0688-0.0717-0.19750.5576-0.09140.2315-0.0567-0.0010.5163-0.07790.361618.12529.127428.9779
53.3946-0.3155.460.2214-0.6448.8873-0.83560.230.498-0.29850.0362-0.2051-0.98150.26130.79941.0012-0.03050.08450.805-0.04860.72086.757523.045814.1015
60.42320.020.44231.4446-1.50568.2034-0.0618-0.13280.20190.0710.01130.2274-0.3129-0.43480.05050.17730.04160.09050.28340.00230.4072-2.510713.07821.5597
70.7664-0.3249-0.81951.902-0.28221.92050.0483-0.11490.0140.42680.17530.08120.03320.4946-0.22360.308-0.0350.05220.5071-0.06430.462410.135715.107132.972
81.18391.58980.3974.32391.47861.73360.1067-0.2330.02290.2551-0.0250.11550.2482-0.1035-0.08170.27620.00840.02680.39210.04170.36150.7422-7.553734.7163
93.61451.99792.10364.315-0.15991.77430.32790.0954-0.41870.00190.0037-0.33640.38090.0302-0.33150.4886-0.0346-0.09140.43020.02010.4959-37.6746-29.448219.6317
102.4912-0.1983.19581.8352-0.23086.90280.1020.05530.1276-0.2663-0.1823-0.35620.29090.48150.08030.26320.01490.09940.23380.00930.328-29.5411-15.529924.6133
112.4555-0.25360.44050.58710.3070.38610.0927-0.1670.14890.20910.0994-0.2220.0247-0.0698-0.19210.3823-0.00480.07640.35640.01210.3585-27.8846-10.607142.1006
120.52360.3888-0.63533.3855-1.26241.5328-0.0065-0.23140.20990.051-0.1543-0.6034-0.0620.24080.16080.26850.02040.00020.4404-0.02510.5811-21.185310.753538.1618
137.5648-0.21692.745415.6282-5.794514.77790.21780.83270.9017-1.6714-0.5011-0.4254-0.56510.54860.28330.4664-0.03780.00030.84350.0040.6838-33.138622.637125.2095
141.57780.09231.66592.7048-2.15418.352-0.1194-0.430.15030.10230.1098-0.0152-0.2627-0.45270.00950.13150.07770.11650.3569-0.03920.2849-42.975912.922933.0859
153.35830.9652-0.64690.515-1.21346.1443-0.057-0.49230.09930.09960.0333-0.03540.2701-0.17310.02360.55460.1922-0.03430.5596-0.03850.4862-30.157515.464343.0547
160.4833-0.17650.30323.86990.51870.81380.1023-0.31840.03090.4462-0.03060.05890.0691-0.2147-0.07170.3274-0.05320.04590.57060.05660.3604-37.9658-7.362546.0288
170.5216-0.9564-0.56633.07671.05280.79990.15170.20030.1088-0.688-0.19340.0268-0.0477-0.12710.04170.44660.0295-0.05760.27150.04150.3475-2.1722-0.3738-3.841
180.276-0.42120.05433.65611.04860.54420.14780.20390.109-0.6045-0.28420.42150.0253-0.00310.13640.46410.0472-0.02960.27870.05940.3813-0.0380.5066-4.354
190.1646-0.3924-0.07683.92410.57560.0980.13080.2065-0.0138-0.8599-0.20380.0854-0.0862-0.06510.0730.62410.03560.02830.2959-0.00780.3814-44.9328-0.66387.9017
200.4188-0.37920.03425.59941.26280.33620.03170.16540.1357-0.4557-0.13860.3701-0.0180.0320.10690.58150.04620.02510.24910.04730.2622-42.84720.20267.1868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 25
2X-RAY DIFFRACTION2A26 - 120
3X-RAY DIFFRACTION3A121 - 161
4X-RAY DIFFRACTION4A162 - 242
5X-RAY DIFFRACTION5B7 - 26
6X-RAY DIFFRACTION6B27 - 119
7X-RAY DIFFRACTION7B120 - 149
8X-RAY DIFFRACTION8B150 - 242
9X-RAY DIFFRACTION9C7 - 25
10X-RAY DIFFRACTION10C26 - 97
11X-RAY DIFFRACTION11C98 - 170
12X-RAY DIFFRACTION12C171 - 242
13X-RAY DIFFRACTION13D7 - 15
14X-RAY DIFFRACTION14D26 - 120
15X-RAY DIFFRACTION15D121 - 148
16X-RAY DIFFRACTION16D149 - 242
17X-RAY DIFFRACTION17E1 - 17
18X-RAY DIFFRACTION18F1 - 17
19X-RAY DIFFRACTION19G1 - 17
20X-RAY DIFFRACTION20H1 - 17

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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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