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- PDB-2iyn: The co-factor-induced pre-active conformation in PhoB -

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Basic information

Entry
Database: PDB / ID: 2iyn
TitleThe co-factor-induced pre-active conformation in PhoB
ComponentsPHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / PHOSPHATE TRANSPORT / ACTIVATOR / SENSORY TRANSDUCTION / PHOSPHATE REGULATION / TWO-COMPONENT REGULATORY SYSTEM / ALPHA/BETA DOUBLY-WOUND 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 / 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 / OTHER / Resolution: 2.08 Å
AuthorsSola, M. / Drew, D.L. / Blanco, A.G. / Gomis-Ruth, F.X. / Coll, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: The Cofactor-Induced Pre-Active Conformation in Phob.
Authors: Sola, M. / Drew, D.L. / Blanco, A.G. / Gomis-Ruth, F.X. / Coll, M.
History
DepositionJul 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
C: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6206
Polymers43,5473
Non-polymers733
Water1,946108
1
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5402
Polymers14,5161
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5402
Polymers14,5161
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5402
Polymers14,5161
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
B: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0804
Polymers29,0322
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-29.6 kcal/mol
Surface area11740 Å2
MethodPISA
5
C: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
hetero molecules

C: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0804
Polymers29,0322
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1310 Å2
ΔGint-30.6 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.742, 105.829, 135.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Mass: 14515.757 Da / Num. of mol.: 3 / Fragment: RECEIVER DOMAIN, RESIDUES 1-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0AFJ5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.55 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.837
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.837 Å / Relative weight: 1
ReflectionResolution: 2.08→45.2 Å / Num. obs: 20372 / % possible obs: 91.4 % / Observed criterion σ(I): 1.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.2

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.194 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.305 658 3.2 %RANDOM
Rwork0.231 ---
obs0.233 19679 91 %-
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: 17.36 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20 Å2
2---2.04 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 3 108 2852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222798
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9763784
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295337
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_restr0.0960.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022121
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21372
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.51716
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40322790
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.35131082
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7334.5994
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: 2.08→2.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 36
Rwork0.259 1189
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)
10.9465-1.73530.22637.67550.25662.7647-0.1074-0.12540.0674-0.13030.2176-0.75730.01780.0494-0.11030.10960.07840.10270.193-0.04130.247533.058-0.57519.047
26.2477-3.2566-0.75925.72210.27290.9919-0.15410.0850.14490.00390.1896-0.0146-0.0576-0.2809-0.03560.17810.10270.06730.22480.03390.025612.2221.55922.735
368.7192-0.7768-5.806838.8206-5.2718-12.10931.01330.91361.0363-1.5383-0.37682.01132.1687-1.8394-0.63650.5829-0.25420.10460.7006-0.15530.5311.7069.66417.655
42.76691.824-0.01064.0039-2.39543.8859-0.16950.04980.16710.3070.0924-0.1379-0.5695-0.06280.07710.39470.0448-0.08950.1784-0.02990.12118.09314.64-4.999
50.64380.1983-2.9023-0.8186-2.1689.9839-0.1594-0.04370.1328-0.3999-0.00080.0898-0.15030.09110.16020.246-0.009-0.02130.24340.04190.215816.7744.92712.869
61.06590.06590.28430.2652-0.43430.6499-0.0166-0.01380.04140.01240.0514-0.00650.0952-0.0711-0.03480.19450.07880.03270.27-0.02780.172520.4219.93413.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 86
2X-RAY DIFFRACTION1A96 - 121
3X-RAY DIFFRACTION2B1 - 84
4X-RAY DIFFRACTION2B98 - 124
5X-RAY DIFFRACTION3B85 - 97
6X-RAY DIFFRACTION4C3 - 84
7X-RAY DIFFRACTION4C97 - 122
8X-RAY DIFFRACTION5A1122
9X-RAY DIFFRACTION5B1125
10X-RAY DIFFRACTION5C1123
11X-RAY DIFFRACTION6A2001 - 2042
12X-RAY DIFFRACTION6B2001 - 2032
13X-RAY DIFFRACTION6C2001 - 2034

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