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- PDB-7p52: GlnK1 from Methanocaldococcus jannaschii with Mg-ATP and 2-oxoglu... -

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Basic information

Entry
Database: PDB / ID: 7p52
TitleGlnK1 from Methanocaldococcus jannaschii with Mg-ATP and 2-oxoglutarate at a resolution of 1.2 A
ComponentsNitrogen regulatory protein GlnK1
KeywordsSIGNALING PROTEIN / PII-family / Methanococcales / methanogenic archaea / hyperthermophile / hydrogenotrophic / nitrogen metabolism / protein regulation / inhibitor / conformational change / T-loop / ATP / 2-oxoglutarate
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 / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / ADENOSINE-5'-TRIPHOSPHATE / NITRATE ION / Nitrogen regulatory protein GlnK1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.20002 Å
AuthorsMueller, M.-C. / Wagner, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Int J Mol Sci / Year: 2021
Title: The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales .
Authors: Muller, M.C. / Wagner, T.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen regulatory protein GlnK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3706
Polymers12,5391
Non-polymers8325
Water3,207178
1
A: Nitrogen regulatory protein GlnK1
hetero molecules

A: Nitrogen regulatory protein GlnK1
hetero molecules

A: Nitrogen regulatory protein GlnK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,11118
Polymers37,6163
Non-polymers2,49515
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 area12760 Å2
ΔGint-58 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.053, 89.053, 98.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-304-

NO3

21A-563-

HOH

31A-570-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrogen regulatory protein GlnK1


Mass: 12538.638 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The formylation on the initial methionine was modelled.
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Tissue: / / Cell: / / Cell line: / / Gene: glnK1, MJ0059 / Organ: / / Plasmid: pET-24b (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q60381

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Non-polymers , 6 types, 183 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 Å3/Da / Density % sol: 58.97 % / Description: Transparent cube
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: GlnK1 was crystallized at 11.2 mg/ml in 25 mM Tris/HCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl on 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). GlnK1 ...Details: GlnK1 was crystallized at 11.2 mg/ml in 25 mM Tris/HCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl on 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). GlnK1 was cocrystallized with 2 mM ATP, 2 mM 2-oxoglutarate and 2 mM MgCl2. Drop of 0.6 ul of protein sample was mixed with 0.6 ul of the crystallization solution. The reservoir contained 90 ul of the following crystallization solution: 20% PEG 3,350, 100 mM Bis-Tris propane pH 8.5 and 200 mM sodium nitrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.2→44.5265 Å / Num. obs: 31673 / % possible obs: 89.8 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 17.8
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.209 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1585 / CC1/2: 0.642 / Rpim(I) all: 0.443 / Rrim(I) all: 1.29 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J9D

2j9d


Resolution: 1.20002→44.5265 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.79 / Stereochemistry target values: ML
Details: The last refinement steps were carried out with hydrogens in riding mode
RfactorNum. reflection% reflection
Rfree0.1554 1550 4.89 %
Rwork0.1311 30118 -
obs0.1324 31668 67.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.74 Å2 / Biso mean: 21.9875 Å2 / Biso min: 9.16 Å2
Refinement stepCycle: final / Resolution: 1.20002→44.5265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 52 178 1108
Biso mean--13.77 37.73 -
Num. residues----112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.240.2605670.20991399146635
1.24-1.280.2331800.19671540162039
1.28-1.330.2361920.19741787187945
1.33-1.40.21621000.1742150225053
1.4-1.470.18371150.14992588270364
1.47-1.560.2078950.15311989208449
1.56-1.680.17422060.13333831403795
1.68-1.850.15132230.129140214244100
1.85-2.120.1471690.11533225339480
2.12-2.650.13951730.11953702387592
2.68-44.530.14672300.1293886411694

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