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- PDB-5u93: Structure of the Regulatory Domain of the AraC Family Transcripti... -

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Basic information

Entry
Database: PDB / ID: 5u93
TitleStructure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR
ComponentsHTH-type transcriptional activator RhaR
KeywordsTRANSCRIPTION / AraC Family / transcriptional Activator / RhaR / Regulatory Domain.
Function / homology
Function and homology information


rhamnose metabolic process / sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Transcription activator HTH, RhaR / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein ...Transcription activator HTH, RhaR / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Homeobox-like domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / beta-L-rhamnopyranose / HTH-type transcriptional activator RhaR
Similarity search - Component
Biological speciesBacteria Latreille et al. 1825 (Bacteria stick insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.999 Å
AuthorsZhao, H.
CitationJournal: To Be Published
Title: Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR
Authors: Lin, J. / Zhao, H. / Shaath, D. / Wehmeye, G. / Kolin, A. / Egan, S.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional activator RhaR
B: HTH-type transcriptional activator RhaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2416
Polymers39,7952
Non-polymers4464
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-10 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.793, 100.793, 95.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HTH-type transcriptional activator RhaR / L-rhamnose operon transcriptional activator RhaR


Mass: 19897.682 Da / Num. of mol.: 2 / Fragment: UNP residues 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteria Latreille et al. 1825 (Bacteria stick insect)
Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: C5A074
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Sugar ChemComp-RM4 / beta-L-rhamnopyranose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LRhapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-rhamnopyranoseCOMMON NAMEGMML 1.0
b-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES pH 6.0, 50 mM Ca(OAc)2, 12 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2016
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. obs: 33840 / % possible obs: 99.78 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 33.128
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.96 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.999→19.863 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.13
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1686 4.98 %0.05
Rwork0.1708 ---
obs0.1724 33840 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.9 Å2 / Biso mean: 41.24 Å2 / Biso min: 14.74 Å2
Refinement stepCycle: final / Resolution: 1.999→19.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 24 188 2812
Biso mean--40.09 48.97 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082690
X-RAY DIFFRACTIONf_angle_d1.0843651
X-RAY DIFFRACTIONf_chiral_restr0.08390
X-RAY DIFFRACTIONf_plane_restr0.004479
X-RAY DIFFRACTIONf_dihedral_angle_d13.652963
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9992-2.0580.25671280.20832638276699
2.058-2.12430.23451400.184526272767100
2.1243-2.20010.21761430.174526392782100
2.2001-2.28810.2241430.172126282771100
2.2881-2.39210.22841400.173226462786100
2.3921-2.5180.22941330.169626772810100
2.518-2.67540.22711330.172326522785100
2.6754-2.88140.19031420.169426792821100
2.8814-3.17030.2181490.169326712820100
3.1703-3.62660.1991420.169826902832100
3.6266-4.560.15451440.153227402884100
4.56-19.86390.21761490.181428673016100
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)
12.97680.40920.28793.86850.28422.94220.0071-0.23670.16360.1148-0.0742-0.0894-0.31130.12790.03130.1998-0.0453-0.04270.17650.01220.157410.0764.79140.979
23.5068-2.96590.83024.2441-0.39941.66260.33520.2288-0.5499-0.3496-0.17410.35560.39430.1669-0.0890.37810.0781-0.0780.2155-0.03480.357715.69936.60624.359
31.4948-0.2187-0.19280.1142-0.15660.5385-0.0645-0.194-0.02310.55730.129-0.15350.2360.25-0.03320.1985-0.0665-0.12230.35050.17810.069513.47350.00533.809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:165 )A6 - 165
2X-RAY DIFFRACTION2( CHAIN B AND RESID 5:165 )B5 - 165
3X-RAY DIFFRACTION3( CHAIN A AND RESID 502:502 ) OR ( CHAIN B AND RESID 202:202 )A502
4X-RAY DIFFRACTION3( CHAIN A AND RESID 502:502 ) OR ( CHAIN B AND RESID 202:202 )B202

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