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- PDB-2vui: Crystal structure of the HupR receiver domain in inhibitory phosp... -

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Basic information

Entry
Database: PDB / ID: 2vui
TitleCrystal structure of the HupR receiver domain in inhibitory phospho- state
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 / ATP binding / cytoplasm
Similarity search - Function
Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / 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 ...Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Hydrogenase transcriptional regulatory protein HupR1
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / 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 / struct_conn / struct_site
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 / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7734
Polymers15,6591
Non-polymers1153
Water0
1
B: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
hetero molecules

B: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5478
Polymers31,3182
Non-polymers2296
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area2610 Å2
ΔGint-21.2 kcal/mol
Surface area16380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.893, 81.893, 61.812
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-1144-

MG

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Components

#1: Protein HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1 / HUPR


Mass: 15658.879 Da / Num. of mol.: 1 / Fragment: RECEIVER DOMAIN, RESIDUES 5-140
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: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Sequence detailsSEQUENCE ENCODES THE RECEIVER DOMAIN OF HUPR

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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: 3.88 Å3/Da / Density % sol: 68.34 % / Description: NONE
Crystal growpH: 8
Details: 2.4 M NACL, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.0, 25% GLYCEROL, 7 MM BECL2, 29 MM NAF

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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 / Details: MIRRORS
RadiationMonochromator: DUAL CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→23.3 Å / Num. obs: 5316 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK1

2jk1


Resolution: 2.9→23.3 Å / SU ML: 0.49 / Phase error: 36.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3202 486 4.8 %
Rwork0.2578 --
obs0.2609 10173 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 123.607 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5627 Å20 Å2-0 Å2
2---0.5627 Å2-0 Å2
3----28.0396 Å2
Refinement stepCycle: LAST / Resolution: 2.9→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 6 0 1080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091097
X-RAY DIFFRACTIONf_angle_d1.2521489
X-RAY DIFFRACTIONf_dihedral_angle_d17.46404
X-RAY DIFFRACTIONf_chiral_restr0.074173
X-RAY DIFFRACTIONf_plane_restr0.004193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.31860.42721700.35523259X-RAY DIFFRACTION100
3.3186-4.17720.34031660.25073263X-RAY DIFFRACTION100
4.1772-23.29960.29161500.24173165X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 23.9264 Å / Origin y: -12.4553 Å / Origin z: -1.2196 Å
111213212223313233
T1.4609 Å20.3157 Å20.1692 Å2-0.9107 Å20.1138 Å2--1.0094 Å2
L4.7655 °2-2.9843 °2-0.4268 °2-3.9102 °22.6171 °2--0.31 °2
S0.6245 Å °-0.0476 Å °0.2868 Å °-0.8409 Å °-0.3162 Å °-0.0668 Å °-0.1426 Å °0.0162 Å °-0.2124 Å °
Refinement TLS groupSelection details: CHAIN B

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