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- PDB-4ozn: GlnK2 from Haloferax mediterranei complexed with ATP -

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Basic information

Entry
Database: PDB / ID: 4ozn
TitleGlnK2 from Haloferax mediterranei complexed with ATP
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN / Glnk2 / PII / GlnB / signaling / Haloferax mediterranei / halophile / archaea
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol
Similarity search - Function
Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / 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 / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / 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'-TRIPHOSPHATE / Nitrogen regulatory protein GlnK2
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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 government 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 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Nitrogen regulatory protein P-II
C: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8789
Polymers45,0693
Non-polymers1,8106
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-87 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.717, 110.717, 76.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLY1AA6 - 4826 - 68
21LEULEUGLYGLY1BB6 - 4826 - 68
31LEULEUGLYGLY1CC6 - 4826 - 68
12LEULEUGLUGLU1AA66 - 10886 - 128
22LEULEUGLUGLU1BB66 - 10886 - 128
32LEULEUGLUGLU1CC66 - 10886 - 128
13ASNASNASNASN3AA109129
23ASNASNASNASN3BB109129
33ASNASNASNASN3CC109129
14ALAALAVALVAL4AA110 - 123130 - 143
24ALAALAVALVAL4CC110 - 123130 - 143

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 15022.854 Da / Num. of mol.: 3
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.5 M Lithium sulphate, 15% PEG 8000 / PH range: 3.2-3.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.44→47.9 Å / Num. obs: 17092 / % possible obs: 100 % / Redundancy: 5.7 % / Net I/σ(I): 8.2

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementResolution: 2.6→44.98 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 15.92 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24348 863 5.1 %RANDOM
Rwork0.21672 ---
obs0.21804 16170 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.43 Å2-0 Å2
2--0.43 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: last / Resolution: 2.6→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 108 28 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192508
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1392.0293436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.24226.06789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5791512
X-RAY DIFFRACTIONr_chiral_restr0.0660.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211812
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5852.4141326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0343.6111647
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1042.7051182
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.52621.3573611
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A300TIGHT THERMAL1.960.5
12B300TIGHT THERMAL1.730.5
13C300TIGHT THERMAL1.660.5
21A307TIGHT THERMAL0.920.5
22B307TIGHT THERMAL2.460.5
23C307TIGHT THERMAL2.220.5
31A4LOOSE POSITIONAL0.035
32B4LOOSE POSITIONAL0.035
33C4LOOSE POSITIONAL0.015
31A4TIGHT THERMAL1.090.5
32B4TIGHT THERMAL0.690.5
33C4TIGHT THERMAL0.510.5
31A4LOOSE THERMAL1.0510
32B4LOOSE THERMAL0.4210
33C4LOOSE THERMAL0.6610
41A99MEDIUM POSITIONAL0.250.5
41A99MEDIUM THERMAL0.722
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 65 -
Rwork0.32 1180 -
obs--99.84 %
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)
12.42770.7376-0.77422.66070.01943.5310.12610.0547-0.16120.0547-0.20650.4919-0.1171-0.52180.08050.1023-0.0576-0.02650.1458-0.03230.1363-46.90136.8294-22.1331
24.31130.5201-0.65852.27320.15412.34730.08260.0839-0.28370.0343-0.02570.20910.0603-0.2174-0.05690.1267-0.0657-0.00960.0732-0.01210.0631-40.782736.1083-22.6201
32.98540.5812-1.28622.0779-0.43544.58150.0426-0.21220.30380.30090.09380.3306-0.3754-0.377-0.13640.10030.00420.06760.1665-0.0580.1222-45.125652.2023-14.1463
41.97520.2705-1.06923.38821.31594.88740.0748-0.28910.25770.1693-0.10530.2069-0.0779-0.2370.03060.0409-0.04630.01550.1529-0.02810.1296-42.127650.891-16.066
53.73821.1825-1.21824.5213-0.87582.39880.2854-0.4544-0.30410.4772-0.1923-0.18490.01890.0696-0.09310.1443-0.0376-0.0250.21280.04810.0691-30.136737.7227-7.4005
63.2496-0.0926-0.45844.6777-0.83032.35360.031-0.3292-0.26140.23440.0188-0.14980.1886-0.0718-0.04980.1098-0.0905-0.02660.21930.03210.0328-30.819639.0979-10.1978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 61
2X-RAY DIFFRACTION2A62 - 123
3X-RAY DIFFRACTION3B5 - 47
4X-RAY DIFFRACTION4B48 - 123
5X-RAY DIFFRACTION5C4 - 58
6X-RAY DIFFRACTION6C59 - 123

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