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- PDB-3pas: Crystal structure of a TetR family transcription regulator (Maqu_... -

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Basic information

Entry
Database: PDB / ID: 3pas
TitleCrystal structure of a TetR family transcription regulator (Maqu_1417) from MARINOBACTER AQUAEOLEI VT8 at 1.90 A resolution
ComponentsTetR family transcription regulator
Keywordstranscription regulator / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


HTH-type transcriptional repressor, 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / S-1,2-PROPANEDIOL / Transcriptional regulator
Similarity search - Component
Biological speciesMarinobacter aquaeolei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TetR family transcription regulator (Maqu_1417) from MARINOBACTER AQUAEOLEI VT8 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: TetR family transcription regulator
B: TetR family transcription regulator
C: TetR family transcription regulator
D: TetR family transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,45321
Polymers90,3644
Non-polymers1,08917
Water8,395466
1
A: TetR family transcription regulator
B: TetR family transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,89913
Polymers45,1822
Non-polymers71811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-16 kcal/mol
Surface area18750 Å2
MethodPISA
2
C: TetR family transcription regulator
D: TetR family transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5538
Polymers45,1822
Non-polymers3716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-19 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.118, 106.180, 117.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
TetR family transcription regulator


Mass: 22590.904 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei (bacteria) / Strain: VT8 / Gene: Maqu_1417 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1U0I5
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.86 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97892
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.9→29.134 Å / Num. obs: 66710 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.903 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.07
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.581.52586412888198.1
1.97-2.050.4042.12582612795199
2.05-2.140.28932458712155199.2
2.14-2.250.21342524912438199.2
2.25-2.390.155.52557712580198.9
2.39-2.580.11672649612995198.8
2.58-2.840.0869.32583312638198.9
2.84-3.250.05314.12587612608199
3.25-4.080.0323.62580712511198.8
4.08-29.1340.02230.62623512700198.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.134 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 6.398 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.135
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.ACETATE (ACT) AND 1,2-PROPANEDIOL (PGO) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 3379 5.1 %RANDOM
Rwork0.1671 ---
obs0.1693 66636 99.78 %-
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: 92.11 Å2 / Biso mean: 32.3405 Å2 / Biso min: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6169 0 73 466 6708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226630
X-RAY DIFFRACTIONr_bond_other_d0.0010.024576
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9529005
X-RAY DIFFRACTIONr_angle_other_deg0.944311062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6255834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82423.023344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.183151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9961563
X-RAY DIFFRACTIONr_chiral_restr0.090.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021494
X-RAY DIFFRACTIONr_mcbond_it2.07933975
X-RAY DIFFRACTIONr_mcbond_other0.64431583
X-RAY DIFFRACTIONr_mcangle_it3.33556375
X-RAY DIFFRACTIONr_scbond_it5.63682655
X-RAY DIFFRACTIONr_scangle_it8.149112595
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 233 -
Rwork0.234 4557 -
all-4790 -
obs--99.03 %
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)
11.88490.1873-0.10660.3021-0.08050.12290.06720.0723-0.1852-0.0435-0.03760.02150.0266-0.0311-0.02960.04330.0003-0.01610.0249-0.00270.03296.105439.42447.6744
20.77460.2131-0.96560.1164-0.0791.86760.0335-0.00020.01160.0017-0.0015-0.004-0.12-0.0132-0.0320.04560.021-0.00070.0173-0.00130.017322.58646.032329.8086
30.58710.15010.61220.04240.11491.68460.01270.0326-0.00040.00410.00160.0020.10160.0417-0.01430.0167-0.00230.00710.0110.00170.011812.019210.786526.7055
40.9039-0.40141.11410.6606-0.7711.5339-0.0662-0.0798-0.03910.05890.16970.1393-0.0951-0.1721-0.10350.03970.03140.03960.0610.0510.1019-7.647321.844439.4431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 191
2X-RAY DIFFRACTION2B3 - 194
3X-RAY DIFFRACTION3C0 - 191
4X-RAY DIFFRACTION4D0 - 191

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