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- PDB-3nrg: Crystal structure of a TetR family transcriptional regulator (Cau... -

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Basic information

Entry
Database: PDB / ID: 3nrg
TitleCrystal structure of a TetR family transcriptional regulator (Caur_2714) from CHLOROFLEXUS AURANTIACUS J-10-FL at 2.56 A resolution
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
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
Regulatory protein TetR
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.56 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TetR family transcriptional regulator (Caur_2714) from CHLOROFLEXUS AURANTIACUS J-10-FL at 2.56 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Feb 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 transcriptional regulator
B: TetR family transcriptional regulator
C: TetR family transcriptional regulator
D: TetR family transcriptional regulator
E: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,67710
Polymers125,5005
Non-polymers1775
Water2,198122
1
A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1352
Polymers25,1001
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1352
Polymers25,1001
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1352
Polymers25,1001
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1352
Polymers25,1001
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1352
Polymers25,1001
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: TetR family transcriptional regulator
hetero molecules

A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2714
Polymers50,2002
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area3020 Å2
ΔGint-39 kcal/mol
Surface area21570 Å2
MethodPISA
7
B: TetR family transcriptional regulator
C: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2714
Polymers50,2002
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-38 kcal/mol
Surface area21620 Å2
MethodPISA
8
D: TetR family transcriptional regulator
E: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2714
Polymers50,2002
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-39 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.933, 204.933, 57.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUGGESTS THAT A MONOMER IS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. CRYSTAL PACKING ANALYSIS INDICATES THAT, IN ADDITION TO THE MONOMER, A DIMER MAY BE STABLE.

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Components

#1: Protein
TetR family transcriptional regulator


Mass: 25099.926 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: Caur_2714 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9WJL5
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 1-216) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-216) 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.71
Details: 25.6% 2-propanol, 0.1M sodium acetate pH 4.71, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97951
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 8, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979511
ReflectionResolution: 2.56→48.536 Å / Num. obs: 38398 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.267 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.24
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.56-2.650.6022.213977375499.8
2.65-2.760.5022.713888385496.4
2.76-2.880.3523.713839367899.9
2.88-3.030.2654.614274379799.9
3.03-3.220.26.214651390699.9
3.22-3.470.1458.213909379398.1
3.47-3.820.09112.114132384698.5
3.82-4.370.06515.614101383198.8
4.37-5.480.05217.9144133876100
5.480.03918.114814406999.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
XSCALEdata scaling
SHELXphasing
SHARPphasing
SOLOMONphasing
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.56→48.536 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. CHLORIDE IONA (CL) FROM THE PROTEIN BUFFER SOLUTION ARE MODELED INTO THE STRUCTURE. 3. PHENIX.XTRIAGE ANALYSIS OF THE DIFFRACTION DATA REVEALS A SIGNIFICANT OFF-ORIGIN PATTERSON PEAK THAT IS 55.4% OF THE ORIGIN PEAK INDICATING PSEUDO-TRANSLATIONAL SYMMETRY RELATING PAIRS OF MONOMERS IN THE ASYMMETRIC UNIT. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1919 5 %RANDOM
Rwork0.207 ---
obs0.209 38373 --
Displacement parametersBiso max: 110.93 Å2 / Biso mean: 46.666 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.933 Å20 Å20 Å2
2---2.933 Å20 Å2
3---5.866 Å2
Refinement stepCycle: LAST / Resolution: 2.56→48.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8582 0 5 122 8709
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3134SINUSOIDAL5
X-RAY DIFFRACTIONt_trig_c_planes241HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1344HARMONIC5
X-RAY DIFFRACTIONt_it8959HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1178SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10327SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8959HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg12209HARMONIC4.50.56
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion15.78
LS refinement shellResolution: 2.56→2.63 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.23 153 5.12 %
Rwork0.214 2836 -
all0.215 2989 -
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)
11.18440.03330.83980.71750.46872.51390.0116-0.11840.05670.07360.0378-0.0231-0.11370.0251-0.0494-0.0636-0.03630.0464-0.01330.0103-0.119111.25656.064729.2622
20.4121-0.19540.35021.3084-1.23774.0781-0.0335-0.0824-0.00090.09260.0061-0.04080.05450.20280.0274-0.03640.03580.0055-0.0602-0.0418-0.134447.0049-31.8563-14.3336
30.9210.0907-0.61930.91950.72642.87250-0.0609-0.00380.0529-0.02180.0508-0.178-0.02090.0219-0.04250.0247-0.0473-0.06870.0528-0.094135.7869-8.7926-14.1358
40.78450.14710.63051.6058-0.73912.87750.0127-0.1075-0.02820.15640.0398-0.14320.11890.0323-0.0526-0.04080.03920.0087-0.0688-0.0097-0.142625.69730.016915.7704
50.7064-0.4046-0.39632.05570.25662.8614-0.0087-0.2021-0.19260.05590.25680.0519-0.134-0.1842-0.248-0.11770.0483-0.0058-0.02320.113-0.14214.446353.059115.9561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 216
2X-RAY DIFFRACTION2{ B|* }B0 - 216
3X-RAY DIFFRACTION3{ C|* }C0 - 216
4X-RAY DIFFRACTION4{ D|* }D0 - 216
5X-RAY DIFFRACTION5{ E|* }E0 - 216

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