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- PDB-2jk1: Crystal structure of the wild-type HupR receiver domain -

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Basic information

Entry
Database: PDB / ID: 2jk1
TitleCrystal structure of the wild-type HupR receiver domain
ComponentsHYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
KeywordsDNA-BINDING / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / BERYLLIUM FLUORIDE PHOSPHORYLATION MIMIC / HUPR / ACTIVATOR / 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
Hydrogenase transcriptional regulatory protein HupR1
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 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 / 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 / _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

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Assembly

Deposited unit
A: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6832
Polymers15,6591
Non-polymers241
Water1,04558
1
A: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
hetero molecules

A: HYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN HUPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3664
Polymers31,3182
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2710 Å2
ΔGint-17.4 kcal/mol
Surface area16320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)89.931, 89.931, 53.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

21A-2043-

HOH

31A-2055-

HOH

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ENCODES THE RECEIVER DOMAIN OF THE HUPR RESPONSE REGULATOR

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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: 3.53 Å3/Da / Density % sol: 65.21 % / 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, AND 0.1% MONO-THIO-GLYCEROL

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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: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→40.22 Å / Num. obs: 12722 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.1→40.23 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.495 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24347 671 5 %RANDOM
Rwork0.22379 ---
obs0.22473 12722 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.488 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 1 58 1150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9591585
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52524.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91915202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2811511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02897
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.2803
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9431.5750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39121169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1943470
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1674.5416
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: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 59
Rwork0.308 914
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)
116.5278-8.2728-3.70078.60564.67042.6072-0.6803-0.1195-0.60170.42910.2450.63130.6131-0.00310.43520.08580.08690.1211-0.11730.0471-0.140335.8916-31.77119.1165
21.61350.8009-0.47892.8046-0.45992.73350.08530.08290.1489-0.3112-0.1174-0.3891-0.08520.36880.0321-0.09490.00610.0967-0.05590.0384-0.059922.2784-1.09866.7048
33.35230.82781.08570.7652-0.94672.9835-0.21080.05430.1169-0.22380.11180.14440.23780.02340.0990.00760.0001-0.0195-0.13060.018-0.1277.8566-4.42034.0437
46.6575-7.9249-2.704210.96583.38881.11720.0056-0.00460.09760.1589-0.0575-0.20370.04560.00240.0519-0.11820.0053-0.0134-0.03530.0298-0.058519.6682-12.268415.5303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A132 - 143
2X-RAY DIFFRACTION2A6 - 83
3X-RAY DIFFRACTION3A84 - 108
4X-RAY DIFFRACTION4A109 - 131

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