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- PDB-4ozj: GlnK2 from Haloferax mediterranei complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 4ozj
TitleGlnK2 from Haloferax mediterranei complexed with ADP
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN / GlnK / PII / GlnB / Signaling / Haloferax mediterranei / halophile / archaea
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytoplasm
Similarity search - Function
Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits ...Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nitrogen regulatory protein GlnK2
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsPalanca, C. / Pedro-Roig, L. / Llacer, J.L. / Camacho, M. / Bonete, M.J. / Rubio, V.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish governmentBFU2011-30407 Spain
Spanish governmentBIO2008_00082 Spain
Valencian governmentPrometeo 2009/51 Spain
CitationJournal: Febs J. / Year: 2014
Title: The structure of a PII signaling protein from a halophilic archaeon reveals novel traits and high-salt adaptations.
Authors: Palanca, C. / Pedro-Roig, L. / Llacer, J.L. / Camacho, M. / Bonete, M.J. / Rubio, V.
History
DepositionFeb 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4502
Polymers15,0231
Non-polymers4271
Water1,29772
1
A: Nitrogen regulatory protein P-II
hetero molecules

A: Nitrogen regulatory protein P-II
hetero molecules

A: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3506
Polymers45,0693
Non-polymers1,2823
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9550 Å2
ΔGint-45 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.185, 89.185, 96.349
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-331-

HOH

31A-332-

HOH

41A-338-

HOH

51A-339-

HOH

61A-340-

HOH

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Components

#1: Protein Nitrogen regulatory protein P-II / PII family protein glnK2


Mass: 15022.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax mediterranei (archaea)
Strain: ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4
Gene: glnK2, HFX_0092, C439_09930 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8ZYW1
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2M ammonium sulphate, 0.1 M NaCitrate, 0.2 M Na/K Tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.32→60.26 Å / Num. obs: 25401 / % possible obs: 96.8 % / Redundancy: 7.7 % / Net I/σ(I): 21.9

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementResolution: 1.45→60.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.367 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18987 1285 5.1 %RANDOM
Rwork0.17338 ---
obs0.17423 23980 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.574 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.96 Å2-0 Å2
2--0.96 Å2-0 Å2
3----3.11 Å2
Refinement stepCycle: last / Resolution: 1.45→60.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 27 72 847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019796
X-RAY DIFFRACTIONr_bond_other_d0.0010.02785
X-RAY DIFFRACTIONr_angle_refined_deg1.4252.0251091
X-RAY DIFFRACTIONr_angle_other_deg1.12531814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3995108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83225.92627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52815131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.083154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02145
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5242.536420
X-RAY DIFFRACTIONr_mcbond_other2.5262.533419
X-RAY DIFFRACTIONr_mcangle_it2.8983.812523
X-RAY DIFFRACTIONr_mcangle_other2.8953.816524
X-RAY DIFFRACTIONr_scbond_it3.3493.022375
X-RAY DIFFRACTIONr_scbond_other3.3473.019376
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1384.365566
X-RAY DIFFRACTIONr_long_range_B_refined4.28221.916860
X-RAY DIFFRACTIONr_long_range_B_other4.13321.314835
X-RAY DIFFRACTIONr_rigid_bond_restr4.31531578
X-RAY DIFFRACTIONr_sphericity_free30.609525
X-RAY DIFFRACTIONr_sphericity_bonded17.76851617
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 86 -
Rwork0.363 1420 -
obs--78.36 %

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