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- PDB-7p4v: GlnK1 from Methanothermococcus thermolithotrophicus with dADP at ... -

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Basic information

Entry
Database: PDB / ID: 7p4v
TitleGlnK1 from Methanothermococcus thermolithotrophicus with dADP at a resolution of 1.94 A
ComponentsGlnK1 from Methanothermococcus thermolithotrophicus
KeywordsSIGNALING PROTEIN / PII-family / Methanococcales / methanogenic archaea / hydrogenotrophs / protein regulation / inhibitor / T-loop / conformational change / dADP / 2-oxoglutarate / nitrogen metabolism
Function / homology2'-DEOXYADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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: GlnK1 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1314
Polymers14,6491
Non-polymers4823
Water41423
1
A: GlnK1 from Methanothermococcus thermolithotrophicus
hetero molecules

A: GlnK1 from Methanothermococcus thermolithotrophicus
hetero molecules

A: GlnK1 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39312
Polymers43,9463
Non-polymers1,4469
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9440 Å2
ΔGint-36 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.296, 87.296, 46.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-202-

CL

21A-203-

CL

31A-323-

HOH

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Components

#1: Protein GlnK1 from Methanothermococcus thermolithotrophicus


Mass: 14648.796 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Strain: DSM 2095 / Tissue: / / Cell: / / Cell line: / / Gene: glnk1 / Organ: / / Variant: / / Plasmid: pET-28a(+) / Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / Variant (production host): /
#2: Chemical ChemComp-DAT / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / DADP


Mass: 411.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O9P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 3.48 Å3/Da / Density % sol: 64.69 % / Description: transparent hexagonal rod
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: GlnK1 crystallized at a concentration of 33 mg/ml in 25 mM TrisHCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl . Drop of 0.6 ul of protein was mixed with 0.6 ul of the ...Details: GlnK1 crystallized at a concentration of 33 mg/ml in 25 mM TrisHCl pH 7.6, 10% glycerol, 2mM dithiothreitol and 500mM NaCl . Drop of 0.6 ul of protein was mixed with 0.6 ul of the crystallization solution in a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The reservoir contained 90 ul of the following crystallization solution: 35 % w/v Pentaerythritol propoxylate (17/8 PO/OH), 100 mM MES pH 6.5, 200 mM Ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.94→75.601 Å / Num. obs: 10108 / % possible obs: 89.1 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.013 / Rrim(I) all: 0.055 / Net I/σ(I): 27.3
Reflection shellResolution: 1.94→2.148 Å / Redundancy: 18.6 % / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 502 / CC1/2: 0.773 / Rpim(I) all: 0.403 / Rrim(I) all: 1.759 / % possible all: 60.2

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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: 1.94→39.3 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.79 / Stereochemistry target values: ML
Details: The last refinement cycle was performed with hydrogens in riding position
RfactorNum. reflection% reflection
Rfree0.2257 492 4.92 %
Rwork0.1966 9503 -
obs0.198 9995 65.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.32 Å2 / Biso mean: 62.7293 Å2 / Biso min: 32.23 Å2
Refinement stepCycle: final / Resolution: 1.94→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 28 23 933
Biso mean--52.82 55.07 -
Num. residues----113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-2.130.4037270.397941143812
2.14-2.440.31941270.30332056218358
2.44-3.080.29891630.26463493365696
3.08-39.30.19731750.16693543371895
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)
13.19260.70910.62362.97750.29744.7612-0.04670.0109-0.2138-0.0249-0.12150.47780.063-1.00580.1030.28480.0084-0.02430.5897-0.01870.421429.28-24.83688.7805
23.01780.58580.333.69360.20744.1599-0.03640.15370.07990.023-0.0210.4285-0.4579-0.65750.05930.3470.0191-0.01350.37850.01990.311734.8314-20.905211.8148
35.55450.0755.48291.6667-0.30945.5014-0.1983-0.1853-0.10590.6613-0.0907-0.2137-0.4938-0.0019-0.15131.29380.10750.05910.47840.00580.611341.4729-4.864629.1679
41.25260.9319-0.06222.28691.80576.8426-0.1704-0.3288-0.27170.44010.097-0.5268-1.10220.2446-0.02491.17220.01220.04060.3465-0.01450.600944.7021-3.754326.6157
52.54190.27020.02592.1201-0.70224.1582-0.10150.22060.1473-0.28260.00120.6813-0.3574-1.15040.08920.36260.0601-0.09440.5567-0.01370.412930.401-21.18484.5921
63.39191.0019-0.15426.2308-2.1693.2020.11770.6905-0.4321-0.6240.36440.43391.5184-0.42490.01540.9255-0.2018-0.010.5556-0.16810.545638.2314-41.5493-0.5484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 22 )A0 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 41 )A23 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 46 )A42 - 46
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 55 )A47 - 55
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 96 )A56 - 96
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 112 )A97 - 112

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