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- PDB-2ia2: The crystal structure of a putative transcriptional regulator RHA... -

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Basic information

Entry
Database: PDB / ID: 2ia2
TitleThe crystal structure of a putative transcriptional regulator RHA06195 from Rhodococcus sp. RHA1
ComponentsPutative Transcriptional RegulatorTranscriptional regulation
KeywordsTRANSCRIPTION / SAD / Transcriptional Regulator / PSI-2 / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


3,4-dihydroxybenzoate metabolic process / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily ...Beta-ketoadipate transcriptional regulator, PcaR/PcaU/PobR / helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, IclR family protein / PcaR
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCymborowski, M.T. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a putative transcriptional regulator RHA06195 from Rhodococcus sp. RHA1
Authors: Cymborowski, M.T. / Chruszcz, M. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Transcriptional Regulator
B: Putative Transcriptional Regulator
C: Putative Transcriptional Regulator
D: Putative Transcriptional Regulator


Theoretical massNumber of molelcules
Total (without water)116,2834
Polymers116,2834
Non-polymers00
Water13,349741
1
A: Putative Transcriptional Regulator
D: Putative Transcriptional Regulator


Theoretical massNumber of molelcules
Total (without water)58,1412
Polymers58,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-34 kcal/mol
Surface area22480 Å2
MethodPISA
2
B: Putative Transcriptional Regulator
C: Putative Transcriptional Regulator


Theoretical massNumber of molelcules
Total (without water)58,1412
Polymers58,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-33 kcal/mol
Surface area22350 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-96 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.892, 121.526, 174.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALARGAA17 - 26517 - 265
21VALARGBB17 - 26517 - 265
12VALLEUCC17 - 26017 - 260
22TYRLEUDD16 - 26016 - 260

NCS ensembles :
ID
1
2
Detailsdimeric first dimer: chains A and D second dimer: chains B and C

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Components

#1: Protein
Putative Transcriptional Regulator / Transcriptional regulation


Mass: 29070.627 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: Q2F1F8, UniProt: Q0SH23*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG3350 25%, 0.2 M LiSulphate, 0.1 M Bis-Tris, 20mM NH4Sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. all: 76498 / Num. obs: 74075 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.066
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3345 / Rsym value: 0.405 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
CCP4phasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
Omodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→36.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.185 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22326 3664 5 %RANDOM
Rwork0.18569 ---
obs0.18758 70206 96.81 %-
all-76498 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 0 741 8061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227422
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.98810102
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1235984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32622.635277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.642151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8041570
X-RAY DIFFRACTIONr_chiral_restr0.1180.21247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23451
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25194
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2568
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9491.54892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69927826
X-RAY DIFFRACTIONr_scbond_it2.95732530
X-RAY DIFFRACTIONr_scangle_it4.3784.52275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1818loose positional0.65
2C1734loose positional0.435
1A1818loose thermal1.1410
2C1734loose thermal1.5610
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 261 -
Rwork0.205 4715 -
obs--90.06 %

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