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- PDB-4ozl: GlnK2 from Haloferax mediterranei complexed with AMP -

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Basic information

Entry
Database: PDB / ID: 4ozl
TitleGlnK2 from Haloferax mediterranei complexed with AMP
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 MONOPHOSPHATE / Nitrogen regulatory protein GlnK2
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4942 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 / Structure summary
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_oper_list / pdbx_struct_special_symmetry / refine_hist / struct_keywords / symmetry
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_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,5624
Polymers15,0231
Non-polymers5393
Water1,09961
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)46,68712
Polymers45,0693
Non-polymers1,6189
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area8880 Å2
ΔGint-38 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.090, 89.090, 95.260
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-202-

SO4

21A-202-

SO4

31A-203-

SO4

41A-328-

HOH

51A-333-

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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2 M 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: I03 / Wavelength: 0.9618 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9618 Å / Relative weight: 1
ReflectionResolution: 1.02→59.96 Å / Num. obs: 23723 / % possible obs: 100 % / Redundancy: 19.9 % / Net I/σ(I): 37.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4942→59.956 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 1217 5.13 %
Rwork0.1614 --
obs0.1625 23722 99.95 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.134 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4563 Å2-0 Å20 Å2
2---2.4563 Å20 Å2
3---4.9125 Å2
Refinement stepCycle: LAST / Resolution: 1.4942→59.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms746 0 33 61 840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006836
X-RAY DIFFRACTIONf_angle_d1.1621155
X-RAY DIFFRACTIONf_dihedral_angle_d14.752317
X-RAY DIFFRACTIONf_chiral_restr0.065146
X-RAY DIFFRACTIONf_plane_restr0.005145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4942-1.5540.27851410.22732477X-RAY DIFFRACTION100
1.554-1.62470.21861410.19142455X-RAY DIFFRACTION100
1.6247-1.71040.22281290.16882481X-RAY DIFFRACTION100
1.7104-1.81760.18261460.14382471X-RAY DIFFRACTION100
1.8176-1.95790.16191360.12352487X-RAY DIFFRACTION100
1.9579-2.15490.15241370.13312490X-RAY DIFFRACTION100
2.1549-2.46680.18341270.15042501X-RAY DIFFRACTION100
2.4668-3.10790.19771320.18212524X-RAY DIFFRACTION100
3.1079-60.0040.17581280.16342619X-RAY DIFFRACTION100

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