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- PDB-7q07: Ketol-acid reductoisomerase from Methanothermococcus thermolithot... -

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Basic information

Entry
Database: PDB / ID: 7q07
TitleKetol-acid reductoisomerase from Methanothermococcus thermolithotrophicus in the open state with NADP and tartrate
ComponentsKetol-Acid Reductoisomerase from Methanothermococcus thermolithotrophicus
KeywordsISOMERASE / Ketol-acid reductoisomerase / KARI / methanogenic archaea / conformational rearrangement / native purification / oligomerization / thermophile / branched-chain amino acid / biosynthesis
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L(+)-TARTARIC ACID
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketol-Acid Reductoisomerase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6197
Polymers36,5571
Non-polymers1,0626
Water2,522140
1
A: Ketol-Acid Reductoisomerase from Methanothermococcus thermolithotrophicus
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)451,42484
Polymers438,68112
Non-polymers12,74372
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
Unit cell
Length a, b, c (Å)130.827, 130.827, 130.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-719-

HOH

21A-763-

HOH

31A-810-

HOH

41A-831-

HOH

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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 , 5 types, 146 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.56 Å3/Da / Density % sol: 51.9 % / Description: Flower-shaped plates.
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: KARI was crystallized at 13.5 mg/ml in the following buffer 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% glycerol. The reservoir was filled with 90 ul crystallization solution (33 % (w/v) ...Details: KARI was crystallized at 13.5 mg/ml in the following buffer 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% glycerol. The reservoir was filled with 90 ul crystallization solution (33 % (w/v) PEG 5000 MME, 100 mM MES/NaOH pH 6.5 and 200 mM ammonium sulphate). Drops of 0.7 ul protein with 0.7 ul of crystallisation solution were applied on the shelf. Crystals were firstly soaked in the crystallisation solution supplemented with 20 mM NADP, 50 mM L-Tartrate and 50 mM MgCl2 for 3 minutes, and then soaked in the crystallisation solution supplemented with 30 % v/v glycerol before freezing.
Temp details: +/- 3 degree

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
Reflection twinOperator: -l,-k,-h / Fraction: 0.12
ReflectionResolution: 2.2→46.25 Å / Num. obs: 19073 / % possible obs: 100 % / Redundancy: 18.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.039 / Rrim(I) all: 0.168 / Net I/σ(I): 23.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2766 / CC1/2: 0.385 / Rpim(I) all: 0.166 / Rrim(I) all: 0.554 / % 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: 7Q03

7q03


Resolution: 2.2→41.37 Å / Cross valid method: THROUGHOUT / σ(F): 133.59 / Phase error: 21.21 / Stereochemistry target values: TWIN_LSQ_F
Details: The refinement was performed with TLS and intensity-based twin refinement with the following twin law -l,-k,-h
RfactorNum. reflection% reflection
Rfree0.2123 1005 5.27 %
Rwork0.1864 18068 -
obs0.19 19073 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.42 Å2 / Biso mean: 30.3423 Å2 / Biso min: 9.07 Å2
Refinement stepCycle: final / Resolution: 2.2→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 49 140 2725
Biso mean--38.5 29.22 -
Num. residues----327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.320.29051500.22712556270694
2.32-2.460.28121580.22522557271594
2.46-2.650.24591180.20772556267496
2.65-2.920.23131450.1792552269795
2.92-3.340.22771320.17432595272795
3.34-4.20.17341530.16262583273694
4.21-41.370.17851490.19152669281895
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)
10.9930.08950.00290.8056-0.06470.7630.04220.04230.03560.20740.0248-0.3021-0.09880.1234-0.05420.1817-0.0663-0.04810.16970.04020.252748.730627.10637.542
20.08350.1118-0.03570.32040.14280.2209-0.009-0.00640.01270.0260.0144-0.03760.03070.00550.00460.06480.0044-0.02860.105-0.00910.094432.71562.58433.7557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 172 )A2 - 172
2X-RAY DIFFRACTION2chain 'A' and (resid 173 through 328 )A173 - 328

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