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- PDB-2rha: Crystal structure of a predicted dna-binding transcriptional regu... -

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Basic information

Entry
Database: PDB / ID: 2rha
TitleCrystal structure of a predicted dna-binding transcriptional regulator (saro_1072) from novosphingobium aromaticivorans dsm at 2.10 A resolution
ComponentsTranscriptional regulator, TetR familyTranscriptional regulation
KeywordsTRANSCRIPTION / Transcription regulator / dna/rna-binding 3-helical bundle fold / helix turn helix motif / hth motif / transcription regulation / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of predicted DNA-binding transcriptional regulator (YP_496351.1) from Novosphingobium aromaticivorans DSM 12444 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,95318
Polymers24,4851
Non-polymers1,46817
Water3,639202
1
A: Transcriptional regulator, TetR family
hetero molecules

A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,90636
Polymers48,9702
Non-polymers2,93634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.837, 102.837, 111.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Transcriptional regulator, TetR family / Transcriptional regulation


Mass: 24485.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: YP_496351.1, Saro_1072 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G9F6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE 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: 6.01 Å3/Da / Density % sol: 79.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 1.6M (NH4)2SO4, 0.1M Citrate pH 5.0, 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: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 26, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.185 Å / Num. obs: 35346 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 39.59 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.154.90.8160.91250825600.816100
2.15-2.214.90.6531.21230625130.653100
2.21-2.284.90.5380.91198124620.538100
2.28-2.354.90.4191.81154123650.419100
2.35-2.424.90.352.21126623020.35100
2.42-2.514.90.2832.61102022500.283100
2.51-2.64.90.2363.21053821540.236100
2.6-2.714.90.1784.11013620790.178100
2.71-2.834.90.1265.8972219890.126100
2.83-2.974.90.1156.3939919290.115100
2.97-3.134.90.0967.2892218220.09699.9
3.13-3.324.80.0847.9839217380.08499.9
3.32-3.554.80.0748.2797616470.07499.9
3.55-3.834.80.069.1728615140.0699.7
3.83-4.24.80.04811.7678914030.04899.7
4.2-4.74.80.04114.2621612950.04199.6
4.7-5.424.80.04612.6543911400.04699.5
5.42-6.644.70.04712.245709740.04799.3
6.64-9.394.60.03218.535647750.03298.7
9.39-29.18540.0320.217424350.0393.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QTQ chain A

2qtq


Resolution: 2.1→29.185 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.432 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE (SO4) AND CITRATE (CIT) IONS FROM THE CRYSTALLIZATION BUFFER AND GLYCEROL (GOL) FROM THE CRYO SOLUTION WERE MODELED INTO THE STRUCTURE. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUES 9 AND 198 WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1772 5 %RANDOM
Rwork0.17 ---
obs0.172 35315 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.675 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---1.16 Å20 Å2
3---2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 88 202 1902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221795
X-RAY DIFFRACTIONr_bond_other_d0.0020.021263
X-RAY DIFFRACTIONr_angle_refined_deg1.6492.012417
X-RAY DIFFRACTIONr_angle_other_deg1.06133052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00522.77183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61415310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9991518
X-RAY DIFFRACTIONr_chiral_restr0.10.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined0.2120.2413
X-RAY DIFFRACTIONr_nbd_other0.1970.21286
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2891
X-RAY DIFFRACTIONr_nbtor_other0.0850.2918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.213
X-RAY DIFFRACTIONr_mcbond_it2.43831183
X-RAY DIFFRACTIONr_mcbond_other0.4813425
X-RAY DIFFRACTIONr_mcangle_it3.21251708
X-RAY DIFFRACTIONr_scbond_it6.5498788
X-RAY DIFFRACTIONr_scangle_it8.36711709
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 125 -
Rwork0.282 2434 -
all-2559 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 27.256 Å / Origin y: 11.8262 Å / Origin z: 51.5333 Å
111213212223313233
T-0.1193 Å20.028 Å20.019 Å2--0.1028 Å2-0.0263 Å2---0.1062 Å2
L0.8988 °20.0022 °20.0219 °2-1.7411 °20.6009 °2--1.3633 °2
S-0.0463 Å °0.0875 Å °-0.1343 Å °0.013 Å °0.0321 Å °-0.1521 Å °0.1962 Å °0.1285 Å °0.0142 Å °

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