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- PDB-8k32: The complex structure of SLKARI with NADH at 2.12-angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 8k32
TitleThe complex structure of SLKARI with NADH at 2.12-angstrom resolution
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsOXIDOREDUCTASE / Complex / ISOMERASE
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesSyntrophothermus lipocalidus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsChen, C.Y. / Huang, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Basic Research Program of China2021YFC2100100 China
CitationJournal: To Be Published
Title: Structural bases of coenzyme specificity of thermophilic ketol-acid reductoisomerase
Authors: Chen, C.Y. / Huang, C.H.
History
DepositionJul 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase (NADP(+))
B: Ketol-acid reductoisomerase (NADP(+))
C: Ketol-acid reductoisomerase (NADP(+))
D: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,03642
Polymers146,7324
Non-polymers5,30438
Water19,4921082
1
A: Ketol-acid reductoisomerase (NADP(+))
B: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,06121
Polymers73,3662
Non-polymers2,69519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-132 kcal/mol
Surface area26300 Å2
MethodPISA
2
C: Ketol-acid reductoisomerase (NADP(+))
D: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,97521
Polymers73,3662
Non-polymers2,60919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-158 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.557, 131.557, 297.906
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-411-

TRS

21A-411-

TRS

31A-511-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ketol-acid reductoisomerase (NADP(+)) / KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase


Mass: 36682.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophothermus lipocalidus (strain DSM 12680 / TGB-C1) (bacteria)
Strain: DSM 12680 / TGB-C1 / Gene: ilvC, Slip_2160 / Production host: Expression vector pET-mod (others)
References: UniProt: D7CJ24, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 6 types, 1120 molecules

#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1082 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1M Bis-Tris, pH 7.2, 0.2M Li2SO4, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→30 Å / Num. obs: 107691 / % possible obs: 99.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 34.01
Reflection shellResolution: 2.12→2.2 Å / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 10855

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→29.09 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 5081 4.8 %
Rwork0.1791 --
obs0.1807 105887 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10253 0 317 1082 11652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810756
X-RAY DIFFRACTIONf_angle_d0.94114613
X-RAY DIFFRACTIONf_dihedral_angle_d19.8171492
X-RAY DIFFRACTIONf_chiral_restr0.0561621
X-RAY DIFFRACTIONf_plane_restr0.0071869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.150.23711440.22572365X-RAY DIFFRACTION70
2.15-2.170.27521180.22972938X-RAY DIFFRACTION84
2.17-2.20.27441420.22463405X-RAY DIFFRACTION97
2.2-2.230.25181450.21083461X-RAY DIFFRACTION100
2.23-2.250.23031750.2243392X-RAY DIFFRACTION100
2.25-2.290.2222030.20663438X-RAY DIFFRACTION100
2.29-2.320.23691430.22193495X-RAY DIFFRACTION100
2.32-2.350.26951860.21363460X-RAY DIFFRACTION100
2.35-2.390.21411560.19443437X-RAY DIFFRACTION100
2.39-2.430.22211520.19773428X-RAY DIFFRACTION100
2.43-2.470.23661690.19453455X-RAY DIFFRACTION100
2.47-2.520.22491750.19333452X-RAY DIFFRACTION100
2.52-2.560.21461890.19683461X-RAY DIFFRACTION100
2.56-2.620.23671960.19973422X-RAY DIFFRACTION100
2.62-2.670.28151980.19963397X-RAY DIFFRACTION100
2.67-2.740.24571840.19813444X-RAY DIFFRACTION100
2.74-2.80.2141550.1923478X-RAY DIFFRACTION100
2.8-2.880.2241780.19623465X-RAY DIFFRACTION100
2.88-2.960.22311730.19043394X-RAY DIFFRACTION100
2.96-3.060.2392080.19313439X-RAY DIFFRACTION100
3.06-3.170.23562130.19513399X-RAY DIFFRACTION100
3.17-3.30.22431590.18053491X-RAY DIFFRACTION100
3.3-3.450.19681580.17433424X-RAY DIFFRACTION100
3.45-3.630.21951560.15783457X-RAY DIFFRACTION100
3.63-3.850.17841730.15283407X-RAY DIFFRACTION99
3.85-4.150.19751780.1453224X-RAY DIFFRACTION94
4.15-4.570.17681680.14133318X-RAY DIFFRACTION96
4.57-5.220.15261760.14443276X-RAY DIFFRACTION95
5.22-6.570.20781570.18253400X-RAY DIFFRACTION98
6.57-29.090.17981540.16113184X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 23.1973 Å / Origin y: -16.1702 Å / Origin z: -0.9732 Å
111213212223313233
T0.2107 Å20.0347 Å2-0.0193 Å2-0.1728 Å20.0456 Å2--0.2066 Å2
L0.3374 °20.126 °20.2319 °2-0.3046 °20.2152 °2--0.5989 °2
S0.0636 Å °-0.0161 Å °-0.1062 Å °0.1449 Å °0.0015 Å °-0.126 Å °0.1976 Å °0.1555 Å °-0.0591 Å °
Refinement TLS groupSelection details: all

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