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- PDB-3rh2: Crystal structure of a TetR-like transcriptional regulator (Sama_... -

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Basic information

Entry
Database: PDB / ID: 3rh2
TitleCrystal structure of a TetR-like transcriptional regulator (Sama_0099) from Shewanella amazonensis SB2B at 2.42 A resolution
ComponentsHypothetical TetR-like transcriptional regulator
KeywordsDNA BINDING PROTEIN / DNA/RNA-binding 3-helical bundle / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-Biology
Function / homology
Function and homology information


Bacterial transcriptional repressor TetR / Bacterial transcriptional repressor / : / Tetracycline Repressor, domain 2 / 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
PHOSPHATE ION / Unknown ligand / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesShewanella amazonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.42 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical TetR-like transcriptional regulator (Sama_0099) from SHEWANELLA AMAZONENSIS SB2B at 2.42 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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
Revision 1.5Oct 16, 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

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Assembly

Deposited unit
A: Hypothetical TetR-like transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,86410
Polymers25,1221
Non-polymers7439
Water68538
1
A: Hypothetical TetR-like transcriptional regulator
hetero molecules

A: Hypothetical TetR-like transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,72920
Polymers50,2432
Non-polymers1,48518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6600 Å2
ΔGint-41 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.536, 123.536, 49.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Hypothetical TetR-like transcriptional regulator


Mass: 25121.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: SB2B / Gene: Sama_0099 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S1Q5
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.4M KH2PO4, 1.6M NaH2PO4, 0.1M Phosphate Citrate pH 4.2, 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: 0.91837,0.97934,0.97915
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
20.979341
30.979151
ReflectionResolution: 2.42→29.118 Å / Num. obs: 15161 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 70.116 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 7.82
Reflection shell

Rmerge(I) obs: 0.025 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.42-2.511.516056290599.8
2.51-2.61215443278099.6
2.61-2.722.914221256799.8
2.72-2.87416046291299.7
2.87-3.055.815394280399.9
3.05-3.287.714812272899.9
3.28-3.6110.614738281199.8
3.61-4.131314705282599.9
4.13-5.1914.814143276499.9
5.1915.814833282298.4

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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
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.42→29.118 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 14.68 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.221
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.PHOSPHATE (PO4) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE LIGAND-BINDING SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 762 5 %RANDOM
Rwork0.2047 ---
obs0.2068 15113 99.74 %-
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: 132.46 Å2 / Biso mean: 65.5524 Å2 / Biso min: 28.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å20 Å2
2---2.09 Å20 Å2
3---4.18 Å2
Refinement stepCycle: LAST / Resolution: 2.42→29.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 54 38 1812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221835
X-RAY DIFFRACTIONr_bond_other_d0.0010.021258
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9672477
X-RAY DIFFRACTIONr_angle_other_deg1.0133055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9915220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75423.97893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9531512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
X-RAY DIFFRACTIONr_mcbond_it2.06731064
X-RAY DIFFRACTIONr_mcbond_other0.4753428
X-RAY DIFFRACTIONr_mcangle_it3.83851719
X-RAY DIFFRACTIONr_scbond_it6.9118771
X-RAY DIFFRACTIONr_scangle_it9.65211752
LS refinement shellResolution: 2.42→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 58 -
Rwork0.366 1025 -
all-1083 -
obs--99.72 %
Refinement TLS params.Method: refined / Origin x: 41.5402 Å / Origin y: 29.9371 Å / Origin z: 13.8352 Å
111213212223313233
T0.2031 Å20.0293 Å20.0345 Å2-0.1792 Å20.1185 Å2--0.1134 Å2
L3.4092 °20.1508 °20.9434 °2-2.4395 °20.6798 °2--1.0418 °2
S0.1025 Å °0.1588 Å °0.0506 Å °-0.2524 Å °-0.1131 Å °-0.2833 Å °-0.0319 Å °0.0036 Å °0.0106 Å °

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