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- PDB-2jb9: PhoB response regulator receiver domain constitutively-active dou... -

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Basic information

Entry
Database: PDB / ID: 2jb9
TitlePhoB response regulator receiver domain constitutively-active double mutant D10A and D53E.
ComponentsPHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
KeywordsTRANSCRIPTION / SENSORY TRANSDUCTION / DNA-BINDING / TWO-COMPONENT REGULATORY SYSTEM / GENE REGULATION / PHOSPHATE TRANSPORT / ACTIVATION OF THE PHO REGULON
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / phosphorelay response regulator activity / regulation of DNA-templated transcription initiation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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 regulon transcriptional regulatory protein PhoB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFerrer-Orta, C. / Arribas-Bosacoma, R. / Kim, S.-K. / Blanco, A.G. / Pereira, P.J.B. / Gomis-Ruth, F.X. / Wanner, B.L. / Coll, M. / Sola, M.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The X-Ray Crystal Structures of Two Constitutively Active Mutants of the E. Coli Phob Receiver Domain Give Insights Into Activation
Authors: Arribas-Bosacoma, R. / Kim, S.-K. / Ferrer-Orta, C. / Blanco, A.G. / Pereira, P.J.B. / Gomis-Ruth, F.X. / Wanner, B.L. / Coll, M. / Sola, M.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Three-Dimensional Crystal Structure of the Transcription Factor Phob Receiver Domain.
Authors: Sola, M. / Gomis-Ruth, F.X. / Serrano, L. / Gonzalez, A. / Coll, M.
History
DepositionDec 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
B: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Theoretical massNumber of molelcules
Total (without water)28,9722
Polymers28,9722
Non-polymers00
Water3,063170
1
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Theoretical massNumber of molelcules
Total (without water)14,4861
Polymers14,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Theoretical massNumber of molelcules
Total (without water)14,4861
Polymers14,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.924, 60.157, 116.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB / PHOB RESPONSE REGULATOR D10A-D53E


Mass: 14485.772 Da / Num. of mol.: 2 / Fragment: RECEIVER DOMAIN, RESIDUES 1-127 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PBAT-4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 10 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASP 53 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, ASP 10 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASP 53 TO GLU ENGINEERED RESIDUE IN CHAIN B, ASP 10 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 53 TO GLU
Sequence detailsMUTATIONS D10A, D53E

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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 Å3/Da / Density % sol: 36.18 %
Crystal growpH: 8
Details: 3 MICROLITER OF PROTEIN SOLUTION AT 5.6 MG/ML AND 6 MICROLITER OF RESERVOIR SOLUTION (22.5% PEG 4K, 0.4 M SODIUM ACETATE, 0.1 M TRISHCL, PH 8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→32.9 Å / Num. obs: 24245 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B00

1b00


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.496 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 638 2.6 %RANDOM
Rwork0.223 ---
obs0.224 23577 92 %-
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: 24.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 0 170 2121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221987
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9832687
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8635241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19823.54296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46515366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3951522
X-RAY DIFFRACTIONr_chiral_restr0.2020.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2988
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21362
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9311.51258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45721975
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3813822
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7164.5712
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 34
Rwork0.308 1810
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)
10.86130.3110.08552.4786-0.63560.9463-0.02260.06170.0332-0.09660.0075-0.02230.0598-0.01030.015-0.0507-0.00220.0022-0.0767-0.0119-0.06312.51137.044827.4109
21.11640.6031-0.17820.58270.11011.79450.0758-0.35290.0565-0.0331-0.1114-0.0491-0.0188-0.15990.0357-0.07630.0061-0.01780.05040.0213-0.0084-4.68990.791256.6935
30.43760.17430.13130.2843-0.15910.62870.0061-0.05810.0152-0.00980.018-0.0549-0.00050.025-0.0241-0.04250.0192-0.0275-0.05920.0067-0.0234-0.09963.98937.8348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 123
2X-RAY DIFFRACTION2B2 - 123
3X-RAY DIFFRACTION3A2001 - 2102
4X-RAY DIFFRACTION3B2001 - 2068

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