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- PDB-3qbm: Crystal structure of a TetR transcriptional regulator (Caur_2221)... -

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Basic information

Entry
Database: PDB / ID: 3qbm
TitleCrystal structure of a TetR transcriptional regulator (Caur_2221) from CHLOROFLEXUS AURANTIACUS J-10-FL at 1.80 A resolution
ComponentsTetR transcriptional regulator
Keywordstranscription regulator / DNA/RNA-BINDING THREE-HELICAL BUNDLE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / TRANSCRIPTION
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain / 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Regulatory protein TetR
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TetR transcriptional regulator (Caur_2221) from CHLOROFLEXUS AURANTIACUS J-10-FL at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_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
Revision 1.4Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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 transcriptional regulator
B: TetR transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,41913
Polymers44,3712
Non-polymers1,04811
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-28 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.335, 106.449, 45.577
Angle α, β, γ (deg.)90.000, 110.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 1 - 198 / Label seq-ID: 2 - 199

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein TetR transcriptional regulator / Regulatory protein TetR


Mass: 22185.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: Caur_2221 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9WFT0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 20.0% PEG-8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97931
ReflectionResolution: 1.8→27.255 Å / Num. all: 34688 / Num. obs: 34688 / % possible obs: 97.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 16.78 Å2 / Rsym value: 0.088 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.852.40.5392.2610925730.53998.9
1.85-1.92.40.4581.5605525410.45898.2
1.9-1.952.40.3751.8581324390.37598.5
1.95-2.012.40.2832.4569623890.28398.5
2.01-2.082.40.2372.6554123270.23798.4
2.08-2.152.40.1744536922350.17498.2
2.15-2.232.40.1554.5505421160.15597.8
2.23-2.322.40.1373.5495520710.13797.8
2.32-2.432.40.1215.7477119950.12198.1
2.43-2.552.40.1016.8458418960.10197.1
2.55-2.682.40.0887.7426317760.08896.7
2.68-2.852.40.0768.9402116720.07696.3
2.85-3.042.40.06610.4381415840.06696
3.04-3.292.40.05412340514420.05495.6
3.29-3.62.30.04414313813460.04494.7
3.6-4.022.30.04512.4277511900.04594.7
4.02-4.652.60.0510.5279610930.0596.4
4.65-5.692.50.0481222869070.04895.7
5.69-8.052.50.0441417997070.04495.6
8.05-27.2552.50.033189653890.03392.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→27.255 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.424 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.13
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.MAGNESIUM (MG) AND POLYETHYLENE GLYCOL FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1730 5 %RANDOM
Rwork0.1647 ---
obs0.1672 34661 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 75.3 Å2 / Biso mean: 23.7212 Å2 / Biso min: 8.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0.03 Å2
2---0.26 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 68 311 3439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223309
X-RAY DIFFRACTIONr_bond_other_d0.0010.022296
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9734491
X-RAY DIFFRACTIONr_angle_other_deg0.96735568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9325436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46622.368152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29315564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2171540
X-RAY DIFFRACTIONr_chiral_restr0.0890.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_mcbond_it1.79532033
X-RAY DIFFRACTIONr_mcbond_other0.5523828
X-RAY DIFFRACTIONr_mcangle_it2.74753290
X-RAY DIFFRACTIONr_scbond_it4.74881276
X-RAY DIFFRACTIONr_scangle_it7.122111180
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2399 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.585
LOOSE THERMAL2.5110
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 129 -
Rwork0.22 2434 -
all-2563 -
obs--98.77 %
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)
10.53870.393-0.1741.1649-0.48620.21930.1159-0.07270.040.2223-0.11060.0097-0.10850.0748-0.00530.0612-0.04820.00490.0634-0.01390.016-7.7506-45.24433.1964
20.49540.5817-0.07071.1147-0.27880.3775-0.00110.04030.0651-0.06750.01150.0741-0.02860.0188-0.01050.0232-0.00060.00390.0302-0.0090.0236-13.2814-47.2505-20.3399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 198
2X-RAY DIFFRACTION2B1 - 198

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