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- PDB-2vuh: Crystal structure of the D55E mutant of the HupR receiver domain -

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Basic information

Entry
Database: PDB / ID: 2vuh
TitleCrystal structure of the D55E mutant of the HupR receiver domain
ComponentsHYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
KeywordsDNA-BINDING / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / BERYLLIUM FLUORIDE PHOSPHORYLATION MIMIC / HUPR / ACTIVATOR / CYTOPLASM / ATP-BINDING / TWO-COMPONENT REGULATORY SYSTEM / TRANSCRIPTION / PHOSPHOPROTEIN / RESPONSE REGULATOR
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / DNA-templated transcription / ATP binding / cytoplasm
Similarity search - Function
NtrC-type HTH DNA-binding domain profile. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / : / AAA+ ATPase lid domain / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family ...NtrC-type HTH DNA-binding domain profile. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / : / AAA+ ATPase lid domain / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Homeobox-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogenase transcriptional regulatory protein HupR1
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, K.M. / Lowe, E.D. / Venien-Bryan, C. / Johnson, L.N.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The Hupr Receiver Domain Crystal Structure in its Nonphospho and Inhibitory Phospho States.
Authors: Davies, K.M. / Lowe, E.D. / Venien-Bryan, C. / Johnson, L.N.
History
DepositionMay 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
B: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1


Theoretical massNumber of molelcules
Total (without water)15,6731
Polymers15,6731
Non-polymers00
Water46826
1
B: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1

B: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1


Theoretical massNumber of molelcules
Total (without water)31,3462
Polymers31,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area2660 Å2
ΔGint-18.7 kcal/mol
Surface area15660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.782, 81.782, 61.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-2005-

HOH

21B-2024-

HOH

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Components

#1: Protein HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1 / HUPR


Mass: 15672.904 Da / Num. of mol.: 1 / Fragment: RECEIVER DOMAIN, RESIDUES 5-140 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26408
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, ASP 55 TO GLU
Sequence detailsSEQUENCE ENCODES THE RECEIVER DOMAIN OF THE HUPR RESPONSE REGULATOR, WITH THE MUTATION D55E

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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: 3.74 Å3/Da / Density % sol: 67.15 % / Description: NONE
Crystal growpH: 8
Details: 2.4 M NACL, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.0, 28% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DUAL CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→24.52 Å / Num. obs: 7797 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK1

2jk1


Resolution: 2.5→24.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.185 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24714 399 4.9 %RANDOM
Rwork0.2207 ---
obs0.22204 7797 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.466 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å21.25 Å20 Å2
2--2.51 Å20 Å2
3----3.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 0 26 1088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9611468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3895134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39723.92251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08815188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6231510
X-RAY DIFFRACTIONr_chiral_restr0.1140.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02814
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.2492
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2726
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5510.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0441.5695
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79721087
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3223436
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9354.5381
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: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 26
Rwork0.334 571

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