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

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Basic information

Entry
Database: PDB / ID: 2jba
TitlePhoB response regulator receiver domain constitutively-active double mutant D53A and Y102C.
Components(PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB) x 2
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / SENSORY TRANSDUCTION / PHOSPHATE REGULATION / TRANSCRIPTION REGULATION / ACTIVATOR / TRANSPORT / DNA-BINDING / CONSTITUTIVELY-ACTIVE MUTANT / TWO-COMPONENT REGULATORY SYSTEM / GENE REGULATION / PHOSPHATE TRANSPORT / ACTIVATION OF THE PHO REGULON / PHOSPHORYLATION / ALPHA/BETA DOUBLY WOUN FOLD
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 profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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 profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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: 1.45 Å
AuthorsArribas-Bosacoma, R. / Ferrer-Orta, C. / 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 Escherichia 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,0205
Polymers28,8512
Non-polymers1683
Water5,459303
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-28 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.907, 47.631, 59.703
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB / PHOB RESPONSE REGULATOR D53A-Y102C


Mass: 14439.729 Da / Num. of mol.: 1 / 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: Protein PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB / PHOB RESPONSE REGULATOR D53A-Y102C


Mass: 14411.716 Da / Num. of mol.: 1 / 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 53 TO ALA ENGINEERED RESIDUE IN CHAIN A, TYR 102 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, ASP 53 TO ALA ENGINEERED RESIDUE IN CHAIN A, TYR 102 TO CYS ENGINEERED RESIDUE IN CHAIN B, ASP 53 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 102 TO CYS
Sequence detailsMUTATIONS D53A,Y102C

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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: 2.2 Å3/Da / Density % sol: 36.92 %
Crystal growpH: 8
Details: 3 MICROLITER OF PROTEIN SOLUTION AT 5.5 MG/ML AND 3 MICROLITER OF RESERVOIR SOLUTION (20% (W/V) PEG 4K, 0.4M SODIUM ACETATE, 0.1M TRISHCL (PH 8), 0.01M DTT

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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: 1.45→58.7 Å / Num. obs: 41827 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3 / % possible all: 70.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B00

1b00


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.224 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 770 1.8 %RANDOM
Rwork0.189 ---
obs0.189 41049 99.9 %-
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: 12.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.32 Å2
2---0.09 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 10 303 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.982731
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.125244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021507
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.51241
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42422025
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4313778
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0954.5706
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: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 36
Rwork0.284 2092
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)
11.3004-0.27460.21351.3871-0.37982.0960.00880.1255-0.0581-0.0747-0.0415-0.00290.0692-0.00230.03260.14490.005-0.0130.1372-0.00080.087212.1960.29821.391
22.59920.785-0.80131.4137-0.02673.25160.1336-0.23740.06980.0714-0.1550.0715-0.1839-0.00760.02140.1566-0.0214-0.01680.1524-0.02320.0515-2.769-0.10348.12
3-0.3302-0.2733-0.4284-0.86150.41060.4258-0.01650.0847-0.1270.0371-0.1644-0.0355-0.1756-0.22160.18090.17060.027-0.01150.1845-0.03340.1634-2.9260.24930.548
429.014333.255716.8625-6.39641.1377-59.27650.0251.5639-1.09071.1595-0.4153-1.40311.54610.85270.39030.1551-0.0051-0.00240.16250.00170.165528.0521.5220.67
50.84370.2536-0.35830.3556-0.28791.00690.03810.01190.0111-0.004-0.0440.0101-0.0118-0.00230.00590.0896-0.0033-0.04360.0537-0.02630.03786.6150.05831.014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 126
2X-RAY DIFFRACTION2B2 - 122
3X-RAY DIFFRACTION3A1127
4X-RAY DIFFRACTION3B1123
5X-RAY DIFFRACTION4A1128
6X-RAY DIFFRACTION5A2001 - 2171
7X-RAY DIFFRACTION5B2001 - 2132

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