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- PDB-7q03: Ketol-acid reductoisomerase from Methanothermococcus thermolithot... -

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Basic information

Entry
Database: PDB / ID: 7q03
TitleKetol-acid reductoisomerase from Methanothermococcus thermolithotrophicus in the close state with NADP and Mg2+
ComponentsKetol-acid reductoisomerase from Methanothermococcus thermolithotrophicus
KeywordsISOMERASE / Ketol-acid reductoisomerase / KARI / methanogenic archaea / conformational rearrangement / native purification / oligomerization / thermophile / branched-chain keto acid / biosynthesis
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLemaire, O.N. / Mueller, M. / Wagner, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Biomolecules / Year: 2021
Title: Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen.
Authors: Lemaire, O.N. / Muller, M.C. / Kahnt, J. / Wagner, T.
History
DepositionOct 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 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: Ketol-acid reductoisomerase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,07212
Polymers36,5571
Non-polymers1,51511
Water1,13563
1
A: Ketol-acid reductoisomerase from Methanothermococcus thermolithotrophicus
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)456,858144
Polymers438,68112
Non-polymers18,177132
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area129520 Å2
ΔGint-1109 kcal/mol
Surface area129550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.882, 129.882, 129.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ketol-acid reductoisomerase from Methanothermococcus thermolithotrophicus


Mass: 36556.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: / / References: ketol-acid reductoisomerase (NADP+)

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Non-polymers , 7 types, 74 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.5 Å3/Da / Density % sol: 50.84 % / Description: Transparent plates
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: The reservoir was filled with 90 ul of crystallisation solution: 20% (w/v) PEG 6000, 100 mM Tris/HCl pH 8.0 and 200 mM lithium chloride. The protein was crystallized at 13 mg/ml in the ...Details: The reservoir was filled with 90 ul of crystallisation solution: 20% (w/v) PEG 6000, 100 mM Tris/HCl pH 8.0 and 200 mM lithium chloride. The protein was crystallized at 13 mg/ml in the following buffer 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% (v/v) glycerol. Drops of 0.7 ul protein with 0.7 ul of crystallisation solution were applied on the shelf. Crystals were soaked in the crystallisation solution supplemented with 30% (v/v) ethylene glycol for few seconds before freezing in liquid nitrogen.
Temp details: +/- 3 degrees

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.73913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73913 Å / Relative weight: 1
Reflection twinOperator: -l,-k,-h / Fraction: 0.32
ReflectionResolution: 2.1→45.92 Å / Num. obs: 21408 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.026 / Rrim(I) all: 0.098 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3090 / CC1/2: 0.468 / Rpim(I) all: 0.212 / Rrim(I) all: 0.774 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TSK

4tsk


Resolution: 2.1→41.07 Å / Cross valid method: THROUGHOUT / σ(F): 39.04 / Phase error: 30.48 / Stereochemistry target values: TWIN_LSQ_F
Details: The refinement was performed with TLS and using intensity-based twin refinement with the following twin law -l,-k,-h
RfactorNum. reflection% reflection
Rfree0.1886 1093 5.11 %
Rwork0.1759 20315 -
obs0.1886 21408 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.52 Å2 / Biso mean: 45.8799 Å2 / Biso min: 23.36 Å2
Refinement stepCycle: final / Resolution: 2.1→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 96 63 2701
Biso mean--50.97 39.99 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.20.26911140.26912552266696
2.2-2.310.25871210.23432518263995
2.31-2.460.23971380.21732505264395
2.46-2.650.23821430.20832519266295
2.65-2.910.25761340.20022538267295
2.91-3.330.20011480.19592516266494
3.34-4.20.19971540.16682533268794
4.21-41.070.16081410.16842634277595
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)
10.51910.22590.51971.0771-0.08660.55250.17370.2837-0.2038-0.28020.3859-0.83950.60160.3669-0.01450.3217-0.05060.04980.6558-0.10.442653.452125.941-1.1575
20.36920.37860.19910.49210.36310.81320.0463-0.08010.00980.18210.0468-0.2328-0.05480.05410.05880.3202-0.0698-0.10580.33130.03890.368348.196525.13258.8463
30.39210.18080.00450.90060.4002-0.1762-0.0720.0051-0.03760.0150.0961-0.12970.11040.1177-0.00250.19180.0197-0.01350.26010.01650.155732.4831.30164.6431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )A2 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 183 )A27 - 183
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 329 )A184 - 329

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