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- PDB-1xhf: Crystal structure of the bef3-activated receiver domain of redox ... -

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Basic information

Entry
Database: PDB / ID: 1xhf
TitleCrystal structure of the bef3-activated receiver domain of redox response regulator arca
ComponentsAerobic respiration control protein arcA
KeywordsTRANSCRIPTION / Two-Component System / Gene Regulation / Transcription Factor / Anoxic Redox Control / Doubly Wound Five-Stranded Beta/Alpha Fold
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription repressor activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / BERYLLIUM DIFLUORIDE / BERYLLIUM TETRAFLUORIDE ION / Aerobic respiration control protein ArcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.152 Å
AuthorsToro-Roman, A. / Mack, T.R. / Stock, A.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the alpha4-beta5-alpha5 Face
Authors: Toro-Roman, A. / Mack, T.R. / Stock, A.M.
History
DepositionSep 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aerobic respiration control protein arcA
B: Aerobic respiration control protein arcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8549
Polymers28,4752
Non-polymers3797
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.169, 86.169, 213.082
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: MSE / Refine code: 6 / Auth seq-ID: 3 - 122 / Label seq-ID: 3 - 122

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsBiological assembly is a homodimer present in the assymetric unit.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aerobic respiration control protein arcA / Redox Response Regulator ArcA / Dye resistance protein


Mass: 14237.452 Da / Num. of mol.: 2 / Fragment: Receiver Domain / Mutation: N123Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: arcA, dye, fexA, sfrA, seg, msp, cpxC / Plasmid: pEF29 (pJES307 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS and BL21(DE3) / References: UniProt: P0A9Q1

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Non-polymers , 5 types, 124 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-BF4 / BERYLLIUM TETRAFLUORIDE ION / Tetrafluoroberyllate


Mass: 85.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF4
#5: Chemical ChemComp-BF2 / BERYLLIUM DIFLUORIDE / Beryllium fluoride


Mass: 47.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.96 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium Acetate, MPD, Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97176 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2004
RadiationMonochromator: KOHZU Double Crystal Monochromator With A Sagittally Focused Second Crystal. Crystal Type Is Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97176 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 26318 / Num. obs: 26280 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 15.1 Å2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2529 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.2phasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model Of ArcA Receiver Domain Without Mg2+/BeF3-

Resolution: 2.152→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.481 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.21219 2641 10.1 %RANDOM
Rwork0.18716 ---
obs0.18978 26206 99.89 %-
all-26260 --
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 mean: 29.168 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.55 Å20 Å2
2--1.09 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.152→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 22 117 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221962
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.982651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675241
X-RAY DIFFRACTIONr_chiral_restr0.1010.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021452
X-RAY DIFFRACTIONr_nbd_refined0.2090.3891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5268
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.516
X-RAY DIFFRACTIONr_mcbond_it1.41721207
X-RAY DIFFRACTIONr_mcangle_it2.43831951
X-RAY DIFFRACTIONr_scbond_it1.9252755
X-RAY DIFFRACTIONr_scangle_it2.93700
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 945 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.345
loose thermal3.2710
LS refinement shellResolution: 2.152→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.256 193
Rwork0.22 1668
obs-1668

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