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- PDB-1yve: ACETOHYDROXY ACID ISOMEROREDUCTASE COMPLEXED WITH NADPH, MAGNESIU... -

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Basic information

Entry
Database: PDB / ID: 1yve
TitleACETOHYDROXY ACID ISOMEROREDUCTASE COMPLEXED WITH NADPH, MAGNESIUM AND INHIBITOR IPOHA (N-HYDROXY-N-ISOPROPYLOXAMATE)
ComponentsACETOHYDROXY ACID ISOMEROREDUCTASE
KeywordsOXIDOREDUCTASE / BRANCHED-CHAIN AMINO ACID BIOSYNTHESIS / MAGNESIUM / NADP / CHLOROPLAST / TRANSIT PEPTIDE
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / NADPH binding / chloroplast / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Ketol-acid reductoisomerase, plant / 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. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...Ketol-acid reductoisomerase, plant / 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. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-HYDROXY-N-ISOPROPYLOXAMIC ACID / Chem-NDP / Ketol-acid reductoisomerase, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsBiou, V. / Dumas, R. / Cohen-Addad, C. / Douce, R. / Job, D. / Pebay-Peyroula, E.
Citation
Journal: EMBO J. / Year: 1997
Title: The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 A resolution.
Authors: Biou, V. / Dumas, R. / Cohen-Addad, C. / Douce, R. / Job, D. / Pebay-Peyroula, E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Crystallographic Data for Acetohydroxy Acid Isomeroreductase from Spinacia Oleracea
Authors: Dumas, R. / Job, D. / Douce, R. / Pebay-Peyroula, E. / Cohen-Addad, C.
History
DepositionOct 11, 1996Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: ACETOHYDROXY ACID ISOMEROREDUCTASE
J: ACETOHYDROXY ACID ISOMEROREDUCTASE
K: ACETOHYDROXY ACID ISOMEROREDUCTASE
L: ACETOHYDROXY ACID ISOMEROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,05323
Polymers228,1824
Non-polymers3,87119
Water32,2291789
1
I: ACETOHYDROXY ACID ISOMEROREDUCTASE
J: ACETOHYDROXY ACID ISOMEROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,29911
Polymers114,0912
Non-polymers1,2089
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-85 kcal/mol
Surface area34230 Å2
MethodPISA
2
K: ACETOHYDROXY ACID ISOMEROREDUCTASE
L: ACETOHYDROXY ACID ISOMEROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,75412
Polymers114,0912
Non-polymers2,66310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-75 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.430, 61.940, 162.540
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0147, 0.426, -0.9046), (0.4399, -0.8097, -0.3884), (-0.8979, -0.4036, -0.1755)56.6408, 20.2801, 71.6206
2given(0.0146, -0.4297, 0.9028), (0.8108, -0.5234, -0.2622), (0.5852, 0.7358, 0.3408)-3.5034, 3.2311, 3.3305
3given(-1, 0.0038, -0.0006), (0.0036, 0.8876, -0.4606), (-0.0012, -0.4606, -0.8876)53.0105, 18.4141, 76.5397

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Components

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Protein , 1 types, 4 molecules IJKL

#1: Protein
ACETOHYDROXY ACID ISOMEROREDUCTASE / KETOACID REDUCTOISOMERASE


Mass: 57045.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: CDNA FROM ACETOHYDROXY ACID / Organelle: PLASTIDS / Plasmid: PKK223.3
Gene (production host): CDNA FROM ACETOHYDROXY ACID ISOMEROREDUCTASE
Production host: Escherichia coli (E. coli)
References: UniProt: Q01292, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 5 types, 1808 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Chemical
ChemComp-HIO / N-HYDROXY-N-ISOPROPYLOXAMIC ACID


Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1789 / 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: 2.45 Å3/Da / Density % sol: 54 %
Description: TEMPERATURE OF DATA COLLECTION : 100K CRYSTAL WAS FLASH FROZEN IN 20% GLYCEROL/MOTHER LIQUOR SOLUTION.
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.8 Mammonium sulfate11
20.1 MTris-HCl11
3IpOHA11
4NADPH1110 ligand molecules/enzyme monomer
511100 ions/enzyme monomerMgCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionNum. obs: 242843 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3.99 % / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.65→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.239 -
Rwork0.197 -
obs0.197 241827
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.4893 Å20 Å20 Å2
2--3.6525 Å20 Å2
3---4.3493 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15697 0 242 1790 17729
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.4389
X-RAY DIFFRACTIONx_mcangle_it21.6201
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM_LIG.DATTOPO_LIG.DAT
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.71
X-RAY DIFFRACTIONx_dihedral_angle_deg20.91
X-RAY DIFFRACTIONx_improper_angle_deg3.12

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