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- PDB-3cwr: Crystal structure of transcriptional regulator of TetR family (YP... -

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Basic information

Entry
Database: PDB / ID: 3cwr
TitleCrystal structure of transcriptional regulator of TetR family (YP_425770.1) from Rhodospirillum rubrum ATCC 11170 at 1.50 A resolution
ComponentsTranscriptional regulator, TetR family
KeywordsTRANSCRIPTION REGULATOR / YP_425770.1 / transcriptional regulator of TetR family / Bacterial regulatory proteins / tetR family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / DNA-binding / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / : / 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 ...Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / : / 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
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of transcriptional regulator of TetR family (YP_425770.1) from Rhodospirillum rubrum ATCC 11170 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 1.4Feb 1, 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 1.5Nov 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: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8137
Polymers45,3672
Non-polymers4465
Water5,819323
1
A: Transcriptional regulator, TetR family
hetero molecules

B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8137
Polymers45,3672
Non-polymers4465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/61
Buried area3120 Å2
ΔGint-20.1 kcal/mol
Surface area16660 Å2
MethodPISA
2
A: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9724
Polymers22,6831
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8423
Polymers22,6831
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.340, 53.340, 234.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Transcriptional regulator, TetR family


Mass: 22683.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Species: Rhodospirillum rubrum / Strain: NCIB 8255 / Gene: YP_425770.1, Rru_A0679 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2RWL2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.1241.99THE STRUCTURE WAS PHASED BY MAD METHODS AT 1.8 A RESOLUTION AND REFINED AT 1.5 A RESOLUTION AGAINST A DATASET COLLECTED FROM A DIFFERENT CRYSTAL.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop5.79NANODROP, 1.27M Ammonium sulfate, 0.1M MES pH 5.79, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop5.64NANODROP, 1.18M Ammonium sulfate, 0.1M MES pH 5.64, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97852
SYNCHROTRONSSRL BL1-520.979137, 0.918381, 0.978532
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDApr 3, 2008Flat mirror (vertical focusing)
ADSC QUANTUM 3152CCDMar 23, 20081m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978521
20.9791371
30.9183811
40.9785321
ReflectionResolution: 1.5→29.285 Å / Num. obs: 59433 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.454 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 17.05
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.550.3662.3201601069295.3
1.55-1.620.2573.2250111320697.5
1.62-1.690.1894.3208161092697.6
1.69-1.780.2046.1268241188498.1
1.78-1.890.1729321121158398.5
1.89-2.040.12113.6403181212399
2.04-2.240.0721.1429971155499.3
2.24-2.560.04427.8434061173399.1
2.56-3.230.0335.8442241192999
3.23-29.2850.02146.1432031197599

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.285 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.747 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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. EDO AND SO4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3001 5.1 %RANDOM
Rwork0.149 ---
obs0.151 59383 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å20 Å2
2--0.79 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 24 327 3277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223008
X-RAY DIFFRACTIONr_bond_other_d0.0030.022073
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9944117
X-RAY DIFFRACTIONr_angle_other_deg1.33735038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3425405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85622.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27915484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6831538
X-RAY DIFFRACTIONr_chiral_restr0.0920.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213384
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02611
X-RAY DIFFRACTIONr_mcbond_it2.19521959
X-RAY DIFFRACTIONr_mcbond_other1.2012776
X-RAY DIFFRACTIONr_mcangle_it3.27543135
X-RAY DIFFRACTIONr_scbond_it5.15961049
X-RAY DIFFRACTIONr_scangle_it6.718968
X-RAY DIFFRACTIONr_rigid_bond_restr2.94435081
X-RAY DIFFRACTIONr_sphericity_free7.6453327
X-RAY DIFFRACTIONr_sphericity_bonded4.39735023
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 224 -
Rwork0.16 4058 -
all-4282 -
obs--96.2 %

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