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- PDB-4le2: Crystal structure of the unphosphorylated receiver domain of DesR... -

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Basic information

Entry
Database: PDB / ID: 4le2
TitleCrystal structure of the unphosphorylated receiver domain of DesR in the active state
ComponentsTranscriptional regulatory protein DesR
KeywordsDNA BINDING PROTEIN / Response regulator / two-component system / transcription factor / receiver domain
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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. ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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
: / PHOSPHATE ION / Transcriptional regulatory protein DesR
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å
AuthorsTrajtenberg, F. / Larrieux, N. / Buschiazzo, A.
CitationJournal: MBio / Year: 2014
Title: Allosteric activation of bacterial response regulators: the role of the cognate histidine kinase beyond phosphorylation.
Authors: Trajtenberg, F. / Albanesi, D. / Ruetalo, N. / Botti, H. / Mechaly, A.E. / Nieves, M. / Aguilar, P.S. / Cybulski, L. / Larrieux, N. / de Mendoza, D. / Buschiazzo, A.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_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: Transcriptional regulatory protein DesR
B: Transcriptional regulatory protein DesR
C: Transcriptional regulatory protein DesR
D: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03115
Polymers60,4334
Non-polymers59811
Water2,666148
1
A: Transcriptional regulatory protein DesR
B: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5638
Polymers30,2172
Non-polymers3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-26 kcal/mol
Surface area11570 Å2
MethodPISA
2
C: Transcriptional regulatory protein DesR
D: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4687
Polymers30,2172
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-20 kcal/mol
Surface area11350 Å2
MethodPISA
3
A: Transcriptional regulatory protein DesR
hetero molecules

B: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5638
Polymers30,2172
Non-polymers3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2520 Å2
ΔGint-25 kcal/mol
Surface area11980 Å2
MethodPISA
4
C: Transcriptional regulatory protein DesR
hetero molecules

D: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4687
Polymers30,2172
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2050 Å2
ΔGint-14 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.350, 63.850, 121.610
Angle α, β, γ (deg.)90.000, 97.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional regulatory protein DesR


Mass: 15108.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: desR, yocG, BSU19200 / Plasmid: pQE80L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10F' / References: UniProt: O34723
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 1 M KH2PO4, 0.1 M HEPES, 2% Glycerol, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 30, 2010 / Details: mirrors
RadiationMonochromator: multilayer mirrors (Varimax-HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.537→120.474 Å / Num. all: 21892 / Num. obs: 21892 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.1 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.54-2.673.50.4221.81071130490.42295.7
2.67-2.843.60.38621087530140.386100
2.84-3.033.60.25231034828470.252100
3.03-3.273.60.1664.5959726420.166100
3.27-3.593.60.1056.6898324620.105100
3.59-4.013.70.0778.9809422100.077100
4.01-4.633.70.05810.9717319640.058100
4.63-5.673.70.05510.5608316650.055100
5.67-8.023.60.05312.5472713000.053100
8.02-38.8153.50.03910.825647390.03999.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→38.81 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.9032 / Occupancy max: 1 / Occupancy min: 0.4 / SU R Cruickshank DPI: 0.384 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1109 5.07 %RANDOM
Rwork0.1845 ---
all0.1863 21868 --
obs0.1863 21868 99.78 %-
Displacement parametersBiso max: 115.11 Å2 / Biso mean: 39.1507 Å2 / Biso min: 13.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.3272 Å20 Å20.8027 Å2
2--6.9529 Å20 Å2
3----4.6257 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.54→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 23 148 3948
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1346SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes564HARMONIC5
X-RAY DIFFRACTIONt_it3876HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion546SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4501SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3876HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5240HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion18.56
LS refinement shellResolution: 2.54→2.66 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2586 128 4.53 %
Rwork0.2156 2696 -
all0.2175 2824 -
obs--99.78 %
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)
12.3442-0.12450.58711.99990.65624.06780.192-0.17440.1140.0633-0.093-0.0253-0.0394-0.293-0.09910.07130.01310.01470.1223-0.01320.082210.0829-11.222116.7812
22.62830.1245-0.39042.398-1.434.7066-0.06190.0466-0.1489-0.1822-0.00890.02820.19070.26030.07080.17030.02180.00030.16270.02070.17528.791-3.7676-0.8848
33.43790.82520.43132.29741.14553.30960.08480.24140.0099-0.1069-0.0735-0.0618-0.06250.0403-0.01130.0651-0.0106-0.04060.14750.02090.131523.44970.906643.3059
43.84150.28320.75722.915-1.02293.7824-0.1702-0.09630.26130.1627-0.03790.153-0.28050.21110.20810.18790.0123-0.02110.21530.0080.189642.21-5.522861.2836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 132
2X-RAY DIFFRACTION2{ B|* }B-1 - 130
3X-RAY DIFFRACTION3{ C|* }C-2 - 131
4X-RAY DIFFRACTION4{ D|* }D0 - 129

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