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- PDB-4xiy: Crystal structure of ketol-acid reductoisomerase from Azotobacter -

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Basic information

Entry
Database: PDB / ID: 4xiy
TitleCrystal structure of ketol-acid reductoisomerase from Azotobacter
ComponentsKetol-acid reductoisomerase
KeywordsOXIDOREDUCTASE / Rossmann fold / KARI
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / 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 / Acetohydroxy acid isomeroreductase, catalytic 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 / Acetohydroxy acid isomeroreductase, catalytic 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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSpatzal, T. / Cahn, J.K.B. / Wiig, J.A. / Einsle, O. / Hu, Y. / Ribbe, M.W. / Arnold, F.H.
CitationJournal: 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.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase
B: Ketol-acid reductoisomerase
C: Ketol-acid reductoisomerase
D: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,62816
Polymers146,7074
Non-polymers92112
Water72140
1
A: Ketol-acid reductoisomerase
B: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8148
Polymers73,3532
Non-polymers4616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-130 kcal/mol
Surface area23660 Å2
MethodPISA
2
C: Ketol-acid reductoisomerase
D: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8148
Polymers73,3532
Non-polymers4616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-135 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.050, 185.050, 185.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 36676.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / ATCC BAA-1303
References: UniProt: C1DFH7, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 6 types, 52 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.83 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: 0.25 M NaCl, 28 % PEG3350 and 0.1 M Bis-Tris, pH 5.5, strictly anaerobic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000, 1.7448
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.74481
ReflectionResolution: 2.5→82.76 Å / Num. obs: 72509 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NP3

1np3


Resolution: 2.5→55.79 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.835 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24377 3656 5.1 %RANDOM
Rwork0.19392 ---
obs0.19646 68666 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.799 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.5→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9964 0 48 40 10052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910254
X-RAY DIFFRACTIONr_bond_other_d0.0050.029991
X-RAY DIFFRACTIONr_angle_refined_deg1.721.95913868
X-RAY DIFFRACTIONr_angle_other_deg1.6553.00122731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.21532
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022281
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7714.5775268
X-RAY DIFFRACTIONr_mcbond_other3.7674.5755267
X-RAY DIFFRACTIONr_mcangle_it5.6396.8516584
X-RAY DIFFRACTIONr_mcangle_other5.6396.8536585
X-RAY DIFFRACTIONr_scbond_it3.9634.864986
X-RAY DIFFRACTIONr_scbond_other3.9634.8594987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2037.1457273
X-RAY DIFFRACTIONr_long_range_B_refined8.14645.7668681
X-RAY DIFFRACTIONr_long_range_B_other8.14645.7658682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 280 -
Rwork0.287 5066 -
obs--99.91 %

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