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- PDB-4xeh: Apo structure of KARI from Ignisphaera aggregans -

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Basic information

Entry
Database: PDB / ID: 4xeh
TitleApo structure of KARI from Ignisphaera aggregans
ComponentsKetol-acid reductoisomerase
KeywordsOXIDOREDUCTASE / Rossmann fold / KARI
Function / homology
Function and homology information


ketol-acid reductoisomerase [NAD(P)+] / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding
Similarity search - Function
ProC C-terminal domain-like fold / ProC C-terminal domain-like fold - #10 / 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. ...ProC C-terminal domain-like fold / ProC C-terminal domain-like fold - #10 / 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 / Helix non-globular / Special / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ketol-acid reductoisomerase (NAD(P)(+))
Similarity search - Component
Biological speciesIgnisphaera aggregans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.391 Å
AuthorsCahn, J.K.B. / Brinkmann-Chen, S. / Arnold, F.H.
Citation
Journal: Biochem.J. / Year: 2015
Title: Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases.
Authors: Cahn, J.K. / Brinkmann-Chen, S. / Spatzal, T. / Wiig, J.A. / Buller, A.R. / Einsle, O. / Hu, Y. / Ribbe, M.W. / Arnold, F.H.
#1: Journal: Metab. Eng. / Year: 2014
Title: Uncovering rare NADH-preferring ketol-acid reductoisomerases.
Authors: Brinkmann-Chen, S. / Cahn, J.K. / Arnold, F.H.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Data collection
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase


Theoretical massNumber of molelcules
Total (without water)38,4661
Polymers38,4661
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ketol-acid reductoisomerase

A: Ketol-acid reductoisomerase


Theoretical massNumber of molelcules
Total (without water)76,9312
Polymers76,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_587x,-y+3,-z+21
Buried area11890 Å2
ΔGint-98 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.065, 67.482, 112.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Ketol-acid reductoisomerase / Acetohydroxy-acid isomeroreductase / Alpha-keto-beta-hydroxylacyl reductoisomerase


Mass: 38465.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ignisphaera aggregans (archaea) / Strain: DSM 17230 / JCM 13409 / AQ1.S1 / Gene: ilvC, Igag_1561 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3)
References: UniProt: E0SRA9, ketol-acid reductoisomerase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M bis-tris pH 6, 22% polyethylene glycol monomethylether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.391→57.849 Å / Num. all: 71148 / Num. obs: 71148 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.044 / Rsym value: 0.038 / Net I/av σ(I): 10.641 / Net I/σ(I): 13.6 / Num. measured all: 245620
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible allRmerge(I) obs
1.391-1.4730.52693589281.0791.6890.687.5
1.47-1.563.70.83553896510.5740.9631.399.60.963
1.56-1.663.51.43201690730.3230.5352.399.10.535
1.66-1.83.82.93188884500.1570.2684.599.40.268
1.8-1.973.55.62731577240.0830.1378.298.40.137
1.97-2.23.8122696471370.0360.0631799.40.063
2.2-2.543.617.72191561670.0230.0425.697.60.04
2.54-3.113.822.72009753410.0160.02837.199.20.028
3.11-4.43.6261454740790.0130.02348.896.50.023
4.4-32.3153.526.7840523820.0110.0251.197.20.02

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
SCALA3.3.21data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDZ

4xdz


Resolution: 1.391→57.849 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2288 / WRfactor Rwork: 0.1716 / FOM work R set: 0.6692 / SU B: 5.417 / SU ML: 0.086 / SU R Cruickshank DPI: 0.0648 / SU Rfree: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 3474 5 %RANDOM
Rwork0.1757 65375 --
obs0.1787 68932 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.14 Å2 / Biso mean: 31.033 Å2 / Biso min: 15.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 1.391→57.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 101 2657
Biso mean---35.2 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192605
X-RAY DIFFRACTIONr_bond_other_d0.0010.022582
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9783506
X-RAY DIFFRACTIONr_angle_other_deg0.93835951
X-RAY DIFFRACTIONr_chiral_restr0.1240.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
X-RAY DIFFRACTIONr_mcbond_it4.1862.6991306
X-RAY DIFFRACTIONr_mcbond_other4.1872.6981305
X-RAY DIFFRACTIONr_mcangle_it4.8634.0691629
X-RAY DIFFRACTIONr_rigid_bond_restr5.9735183
X-RAY DIFFRACTIONr_sphericity_free27.868534
X-RAY DIFFRACTIONr_sphericity_bonded17.64755208
LS refinement shellResolution: 1.391→1.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 212 -
Rwork0.391 3724 -
all-3936 -
obs--76.04 %

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