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- PDB-3s5r: Crystal structure of a putative transcriptional regulator of the ... -

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Basic information

Entry
Database: PDB / ID: 3s5r
TitleCrystal structure of a putative transcriptional regulator of the TETR family (SYN_02108) from Syntrophus aciditrophicus at 2.60 A resolution
ComponentsTranscriptional regulator TetR family
KeywordsDNA BINDING PROTEIN / DNA/RNA-binding 3-helical bundle / Tetracyclin repressor-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


: / 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 / Transcriptional regulator TetR family
Similarity search - Component
Biological speciesSyntrophus aciditrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative transcriptional regulator of the TetR family (SYN_02108) from Syntrophus aciditrophicus SB at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: 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
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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator TetR family
B: Transcriptional regulator TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2987
Polymers48,8552
Non-polymers4425
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-27 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.433, 110.721, 126.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Transcriptional regulator TetR family


Mass: 24427.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophus aciditrophicus (bacteria) / Strain: SB / Gene: SYNAS_10510, SYN_02108 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2LS68
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15.00% Glycerol, 8.500% iso-Propanol, 17.00% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 9, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
ReflectionResolution: 2.6→29.279 Å / Num. obs: 16314 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.791 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.690.6271.764543000199
2.69-2.80.4842.166903117199.2
2.8-2.930.3582.867023120199.1
2.93-3.080.2513.964012980198.9
3.08-3.270.1655.865453043199.2
3.27-3.520.0998.765543056198.9
3.52-3.880.0612.666943123198.5
3.88-4.430.03519.164623000197.7
4.43-5.570.0282464292995196.5
5.57-29.2790.02129.163872987194.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→29.279 Å / Cor.coef. Fo:Fc: 0.9267 / Cor.coef. Fo:Fc free: 0.9239 / Occupancy max: 1 / Occupancy min: 0.5 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. PEG-4000 FRAGMENTS(PEG) FROM THE CRYSTALLIZATION CONDITION AND 1,2 ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE REFINEMENT WAS RESTRAINED WITH THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 826 5.07 %RANDOM
Rwork0.2426 ---
obs0.2432 16290 --
Displacement parametersBiso max: 186.07 Å2 / Biso mean: 82.9865 Å2 / Biso min: 49.02 Å2
Baniso -1Baniso -2Baniso -3
1--14.5585 Å20 Å20 Å2
2--2.7277 Å20 Å2
3---11.8308 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 29 7 2961
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1398SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes437HARMONIC5
X-RAY DIFFRACTIONt_it2993HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
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_contact3568SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3011HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4092HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion2.05
LS refinement shellResolution: 2.6→2.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3097 162 5.53 %
Rwork0.2579 2770 -
all0.2604 2932 -
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)
10.46020.1146-1.43732.41010.74018.32520.0189-0.090.1266-0.03030.0183-0.1537-0.4150.3029-0.03720.30470.0153-0.0598-0.3044-0.0244-0.280118.128228.903790.8199
20.3928-0.92450.58155.6623-0.91343.1669-0.06660.0132-0.23410.10320.06340.29020.02780.07230.00310.3050.03380.0827-0.30420.0514-0.304219.414610.466778.0009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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