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- PDB-7rdu: Crystal structure of Campylobacter jejuni keto said reductoisomer... -

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Basic information

Entry
Database: PDB / ID: 7rdu
TitleCrystal structure of Campylobacter jejuni keto said reductoisomerase in complex with magnesium and oxidixized and reduced NADPH
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsOXIDOREDUCTASE / magnesium dependent / NADPH dependent / amino acid biosynthesis / biofuel production / dodecamer
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-NDP / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsGuddat, L.W. / You, L.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)114729 Australia
CitationJournal: To Be Published
Title: Multi-faceted approach for the engineering of enzyme variants with improved properties for industrial applications
Authors: Lv, Y. / Guddat, L.
History
DepositionJul 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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 (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2745
Polymers35,7371
Non-polymers1,5374
Water66737
1
A: Ketol-acid reductoisomerase (NADP(+))
hetero molecules

A: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,54910
Polymers71,4742
Non-polymers3,0758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area16470 Å2
ΔGint-149 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.108, 130.108, 130.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

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Components

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


Mass: 35737.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter)
Strain: RM1221 / Gene: ilvC, CJE0735 / Production host: Escherichia (bacteria)
References: UniProt: Q5HVD9, ketol-acid reductoisomerase (NADP+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The buffer was 0.2 M KNO3, 20% PEG3350. The well solution (which was not added to the drop) was 35% PEG3350, 250 mM MgCl2, 20 mM Tris-HCl pH 8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.1 Å / Num. obs: 12712 / % possible obs: 99.2 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.039 / Net I/σ(I): 35.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 7 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 554 / Rpim(I) all: 0.603 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPO

4ypo


Resolution: 2.502→46 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1284 10.1 %
Rwork0.1952 --
obs0.2014 12708 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 98 37 2638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032672
X-RAY DIFFRACTIONf_angle_d0.6343625
X-RAY DIFFRACTIONf_dihedral_angle_d11.717991
X-RAY DIFFRACTIONf_chiral_restr0.022408
X-RAY DIFFRACTIONf_plane_restr0.002458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5021-2.60220.37791320.281189X-RAY DIFFRACTION93
2.6022-2.72070.43921390.29671241X-RAY DIFFRACTION100
2.7207-2.86410.27641450.24041278X-RAY DIFFRACTION100
2.8641-3.04350.33961380.25191267X-RAY DIFFRACTION100
3.0435-3.27840.32521390.24731262X-RAY DIFFRACTION100
3.2784-3.60820.28071430.21021281X-RAY DIFFRACTION100
3.6082-4.13010.24521470.18151274X-RAY DIFFRACTION100
4.1301-5.20230.21131480.171304X-RAY DIFFRACTION100
5.2023-460.21131530.15671328X-RAY DIFFRACTION100

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