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- PDB-7lat: Campylobacter jejuni keto-acid reductoisomerase in complex with Mg2+ -

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Basic information

Entry
Database: PDB / ID: 7lat
TitleCampylobacter jejuni keto-acid reductoisomerase in complex with Mg2+
ComponentsKetol-acid reductoisomerase
KeywordsISOMERASE / metalloenzyme / reductoisomerase
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / 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
Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsGuddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210101802 Australia
CitationJournal: Acs Catalysis / Year: 2024
Title: Mapping of the Reaction Trajectory catalyzed by Class I Ketol-Acid Reductoisomerase
Authors: Lin, X. / Lonhienne, T. / Lv, Y. / Kurz, J. / McGeary, R. / Schenk, G. / Guddat, L.W.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 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
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9173
Polymers35,8681
Non-polymers492
Water1,892105
1
A: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8346
Polymers71,7362
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11590 Å2
ΔGint-134 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.746, 128.746, 128.746
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

21A-588-

HOH

31A-591-

HOH

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Components

#1: Protein Ketol-acid reductoisomerase


Mass: 35868.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ilvC, CW563_00670 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5T0UG45
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ppt buffer 0.2 M Li2SO4, 0.1 M Bis-Tris pH 5.5, 20% PEG3350. The well solution (which was not added to the drop) 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 1, 2016
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→45.52 Å / Num. obs: 12844 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.5 % / Biso Wilson estimate: 37.3319105008 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.027 / Net I/σ(I): 20.9
Reflection shellResolution: 2.47→2.59 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1441 / Rpim(I) all: 0.178 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPO

4ypo


Resolution: 2.47→45.52 Å / SU ML: 0.26725473031 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4152515085
RfactorNum. reflection% reflection
Rfree0.217646181219 1288 10.0295904065 %
Rwork0.1588 11554 -
obs0.1647 12842 99.8755638513 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.3898217922 Å2
Refinement stepCycle: LAST / Resolution: 2.47→45.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 2 105 2610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003737015961562544
X-RAY DIFFRACTIONf_angle_d0.7427523302113429
X-RAY DIFFRACTIONf_chiral_restr0.0261464555369388
X-RAY DIFFRACTIONf_plane_restr0.00280897800039444
X-RAY DIFFRACTIONf_dihedral_angle_d12.6459488706938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.57220.2670553304951420.1848877880561257X-RAY DIFFRACTION98.8692579505
2.5722-2.68920.2638618995261380.1917865378681271X-RAY DIFFRACTION100
2.6892-2.8310.2682200909951400.1738610887111262X-RAY DIFFRACTION100
2.831-3.00830.2629638566621420.1776702125331288X-RAY DIFFRACTION100
3.0083-3.24050.2471956413951430.1774288732161261X-RAY DIFFRACTION100
3.2405-3.56650.2372746284541430.1626379562541288X-RAY DIFFRACTION100
3.5665-4.08230.1882577798841410.1444930575891281X-RAY DIFFRACTION100
4.0823-5.14210.1786569137011470.1409607040711296X-RAY DIFFRACTION100
5.1421-45.51858482530.1971787465591520.1502063021941350X-RAY DIFFRACTION100

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