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- PDB-1mvo: Crystal structure of the PhoP receiver domain from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1mvo
TitleCrystal structure of the PhoP receiver domain from Bacillus subtilis
ComponentsPhoP response regulator
KeywordsTRANSCRIPTION / PHOSPHATE REGULON / TRANSCRIPTIONAL REGULATORY PROTEIN / ALPHA/BETA DOUBLY WOUND FOLD / RESPONSE REGULATOR / PHOSPHORYLATION / ASYMMETRIC INTERFACE / TANDEM ASSOCIATION / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


phosphate ion transport / phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytosol
Similarity search - Function
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 / 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. ...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 / 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
: / Alkaline phosphatase synthesis transcriptional regulatory protein PhoP
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBirck, C. / Chen, Y. / Hulett, F.M. / Samama, J.P. / Structural Proteomics in Europe (SPINE)
Citation
Journal: J.BACTERIOL. / Year: 2003
Title: The Crystal Structure of the Phosphorylation Domain in PhoP Reveals a Functional Tandem Association Mediated by an Asymmetric Interface
Authors: Birck, C. / Chen, Y. / Hulett, F.M. / Samama, J.P.
#1: Journal: J.BACTERIOL. / Year: 2003
Title: Residue R113 Is Essential for PhoP Dimerization and Function: a Residue Buried in the Asymmetric PhoP Dimer Interface Determined in the PhoPN Three-Dimensional Crystal Structure
Authors: Chen, Y. / Birck, C. / Samama, J.P. / Hulett, F.M.
History
DepositionSep 26, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PhoP response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6484
Polymers15,5471
Non-polymers1013
Water3,135174
1
A: PhoP response regulator
hetero molecules

A: PhoP response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2968
Polymers31,0942
Non-polymers2026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x+1/2,-y+3/2,-z+3/41
Unit cell
Length a, b, c (Å)45.704, 45.704, 134.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation : x+1/2, -y+3/2, -z+3/4

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Components

#1: Protein PhoP response regulator / Alkaline phosphatase synthesis transcriptional regulatory protein phoP


Mass: 15546.987 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PHOP / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13792
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 10000, sodium citrate, PEG MME 550, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
123-25 %PEG100001reservoir
20.1 Msodium citrate1reservoirpH5.8
33 %PEG550 MME1reservoir
420 mMTris1droppH7.8
5150 mM1dropNaCl
60.1 mMEDTA1drop
71 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2000
RadiationMonochromator: SAGITALLY FOCUSED Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→27 Å / Num. all: 18122 / Num. obs: 18122 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2775 / Rsym value: 0.187 / % possible all: 92
Reflection
*PLUS
Lowest resolution: 27.1 Å / Num. obs: 18249 / % possible obs: 92 % / Num. measured all: 224913
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Metal-free PhoPN structure solved by MAD

Resolution: 1.6→27 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used weighted full matrix maximum likelihood procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.232 878 -RANDOM
Rwork0.186 ---
all0.188 17226 --
obs0.188 17226 91.7 %-
Displacement parametersBiso mean: 17.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 3 174 1114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_length0.016
X-RAY DIFFRACTIONr_bond_angle1.661
X-RAY DIFFRACTIONr_torsion_angles, period14.503
X-RAY DIFFRACTIONr_torsion_angles, period315.508
X-RAY DIFFRACTIONr_chiral_center_restraints0.1
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection% reflection
Rfree0.22 72 -
Rwork0.14 --
obs-1354 99.86 %
Refinement
*PLUS
Lowest resolution: 27.1 Å / Num. reflection obs: 17225 / Rfactor Rfree: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS

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