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- PDB-5ic5: Bacteriophytochrome response regulator RtBRR -

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Basic information

Entry
Database: PDB / ID: 5ic5
TitleBacteriophytochrome response regulator RtBRR
ComponentsCandidate response regulator, CheY
KeywordsSIGNALING PROTEIN / bacteriophytochrome / response regulator / stable dimer / two component system
Function / homology
Function and homology information


phosphorelay signal transduction system / metal ion binding
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Candidate response regulator, CheY
Similarity search - Component
Biological speciesRamlibacter tataouinensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBaker, A.W. / Satyshur, K.A. / Forest, K.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1256259 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008349-23 United States
National Science Foundation (NSF, United States)MCB 1518160 United States
CitationJournal: J.Bacteriol. / Year: 2016
Title: Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction.
Authors: Baker, A.W. / Satyshur, K.A. / Moreno Morales, N. / Forest, K.T.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionMar 2, 2016ID: 5BRI
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns ...pdbx_struct_conn_angle / reflns / reflns_shell / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_symmetry / _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 / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_conn.pdbx_dist_value / _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_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_symmetry
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Candidate response regulator, CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0286
Polymers18,6711
Non-polymers3585
Water2,216123
1
A: Candidate response regulator, CheY
hetero molecules

A: Candidate response regulator, CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,05612
Polymers37,3412
Non-polymers71510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area3310 Å2
ΔGint-131 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.714, 47.714, 193.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-205-

CAC

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Components

#1: Protein Candidate response regulator, CheY


Mass: 18670.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramlibacter tataouinensis (strain ATCC BAA-407 / DSM 14655 / LMG 21543 / TTB310) (bacteria)
Strain: ATCC BAA-407 / DSM 14655 / LMG 21543 / TTB310 / Gene: Rta_25480 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F5Y2U8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: zinc acetate, sodium cacodylate, magnesium chloride, isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.83→38.3 Å / Num. obs: 37570 / % possible obs: 99.8 % / Redundancy: 1.81 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.034 / Net I/σ(I): 22.87
Reflection shellResolution: 1.83→1.95 Å / Redundancy: 1.81 % / Mean I/σ(I) obs: 1.13 / Rsym value: 0.664 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data reduction
PHENIX1.9_1690phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.3 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.69
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 3245 9.64 %random
Rwork0.1752 ---
obs0.179 33646 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 9 123 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171437
X-RAY DIFFRACTIONf_angle_d1.6441921
X-RAY DIFFRACTIONf_dihedral_angle_d16.615539
X-RAY DIFFRACTIONf_chiral_restr0.083222
X-RAY DIFFRACTIONf_plane_restr0.007253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.92850.40361380.31461351X-RAY DIFFRACTION100
1.9285-1.95860.26441390.29021300X-RAY DIFFRACTION100
1.9586-1.99070.35261420.25391350X-RAY DIFFRACTION100
1.9907-2.0250.30121350.24421283X-RAY DIFFRACTION100
2.025-2.06190.30011460.22341342X-RAY DIFFRACTION100
2.0619-2.10150.24741470.22251309X-RAY DIFFRACTION100
2.1015-2.14440.29061380.21531313X-RAY DIFFRACTION100
2.1444-2.1910.23411400.19351341X-RAY DIFFRACTION100
2.191-2.2420.26141420.19851305X-RAY DIFFRACTION100
2.242-2.2980.22921400.18411324X-RAY DIFFRACTION100
2.298-2.36020.23321420.17871339X-RAY DIFFRACTION100
2.3602-2.42960.24551440.18921312X-RAY DIFFRACTION100
2.4296-2.5080.19671450.18171347X-RAY DIFFRACTION100
2.508-2.59760.2441280.18431310X-RAY DIFFRACTION100
2.5976-2.70160.27071420.19321319X-RAY DIFFRACTION100
2.7016-2.82450.26821490.18041311X-RAY DIFFRACTION100
2.8245-2.97340.25961400.1751326X-RAY DIFFRACTION100
2.9734-3.15960.22391390.18661319X-RAY DIFFRACTION100
3.1596-3.40340.20121410.16641327X-RAY DIFFRACTION100
3.4034-3.74570.21061430.15191315X-RAY DIFFRACTION100
3.7457-4.2870.15531450.14541314X-RAY DIFFRACTION100
4.287-5.39880.17551430.13471320X-RAY DIFFRACTION100
5.3988-38.3660.15881370.1751324X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.0602 Å / Origin y: 25.9874 Å / Origin z: 81.1031 Å
111213212223313233
T0.2047 Å2-0.0397 Å20.0294 Å2-0.1636 Å2-0.0127 Å2--0.1781 Å2
L1.9205 °2-0.73 °2-0.1445 °2-0.8896 °20.0999 °2--1.2934 °2
S-0.0084 Å °-0.024 Å °-0.0732 Å °-0.0232 Å °0.0046 Å °0.0818 Å °0.0661 Å °-0.1288 Å °0.0102 Å °
Refinement TLS groupSelection details: all

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