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- PDB-3ppb: Crystal structure of a putative tetR family transcription regulat... -

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Basic information

Entry
Database: PDB / ID: 3ppb
TitleCrystal structure of a putative tetR family transcription regulator (Shew_3104) from SHEWANELLA SP. PV-4 at 2.10 A resolution
Componentsputative tetR family transcription regulator
KeywordsTRANSCRIPTION REGULATOR / DNA-BINDING / HELIX-TURN-HELIX MOTIF / HTH MOTIF / DNA/RNA-BINDING 3- HELICAL BUNDLE FOLD / TETRACYCLIN REPRESSOR-LIKE FOLD / TRANSCRIPTION / TRANSCRIPTION REGULATION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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 ...DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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 speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative tetR family transcription regulator (Shew_3104) from SHEWANELLA SP. PV-4 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: 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 / 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 1.4Nov 20, 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: putative tetR family transcription regulator
B: putative tetR family transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,76920
Polymers44,1762
Non-polymers1,59318
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint6 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.762, 60.042, 107.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative tetR family transcription regulator


Mass: 22087.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: PV-4 / Gene: Shew_3104 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QHM2

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Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NaCl, 30.0% PEG-400, 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: 0.97903
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.1→28.919 Å / Num. all: 22569 / Num. obs: 22569 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rsym value: 0.119 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.154.90.8211.9807216550.821100
2.15-2.214.90.6932.2779415970.693100
2.21-2.284.90.5192.8750915400.519100
2.28-2.354.90.4743744315280.474100
2.35-2.424.90.4133.3712314580.413100
2.42-2.514.90.3623.9705614390.362100
2.51-2.64.90.2924.6669013720.292100
2.6-2.714.90.2445.4641013160.244100
2.71-2.834.90.1986.5622712790.198100
2.83-2.974.90.177.3591412120.17100
2.97-3.134.80.1478.4560111580.147100
3.13-3.324.90.11210.4544411210.112100
3.32-3.554.80.09213.6496610290.092100
3.55-3.834.80.07216.447849870.072100
3.83-4.24.80.06417.943019010.064100
4.2-4.74.80.05719.939378270.05799.9
4.7-5.424.70.06418.534667320.06499.9
5.42-6.644.60.07516.928966230.07599.7
6.64-9.394.60.05720.423035060.05799.5
9.39-28.91940.04721.711652890.04795.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.3.15data processing
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→28.919 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.9471 / Occupancy max: 1 / Occupancy min: 0.37 / 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. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. CHLORIDE (CL) AND PEG-400 FRAGMENTS (PEG AND PG4) FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. THE SAD PHASES WERE INCLUDED AS ADDITIONAL REFINEMENT RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1152 5.12 %RANDOM
Rwork0.1742 ---
obs0.176 22520 --
Displacement parametersBiso max: 112.57 Å2 / Biso mean: 40.4333 Å2 / Biso min: 16.45 Å2
Baniso -1Baniso -2Baniso -3
1--5.0643 Å20 Å20 Å2
2--0.5459 Å20 Å2
3---4.5184 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 102 124 3186
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1501SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes472HARMONIC5
X-RAY DIFFRACTIONt_it3201HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion403SEMIHARMONIC5
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_contact3830SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3201HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4309HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion2.78
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2466 146 4.93 %
Rwork0.2079 2816 -
all0.2098 2962 -
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)
11.28520.0936-0.04840.7012-0.10662.25970.04960.2571-0.0392-0.09260.0083-0.1589-0.00980.173-0.05790.00790.01940.0173-0.04580.0254-0.151234.45510.030160.5398
20.94010.33341.04080.3436-0.12792.450.016-0.04820.0076-0.03740.02070.1159-0.0877-0.0762-0.03670.08150.0116-0.0266-0.0921-0.006-0.111513.7411-1.082366.2564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|7 - A|194 }A7 - 194
2X-RAY DIFFRACTION2{ B|7 - B|194 }B7 - 194

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