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- PDB-3fr7: ketol-acid reductoisomerase (KARI) in complex with Mg2+ -

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Basic information

Entry
Database: PDB / ID: 3fr7
Titleketol-acid reductoisomerase (KARI) in complex with Mg2+
ComponentsPutative ketol-acid reductoisomerase (Os05g0573700 protein)
KeywordsOXIDOREDUCTASE / Rossmann fold / NADPH / Knotted protein / branched-chain amino acid biosynthesis / Isomerase
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
Ketol-acid reductoisomerase, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGuddat, L.W. / Leung, E.W.W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Conformational changes in a plant ketol-acid reductoisomerase upon Mg(2+) and NADPH binding as revealed by two crystal structures
Authors: Leung, E.W. / Guddat, L.W.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 26, 2012Group: Refinement description
Revision 1.3Sep 6, 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_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_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
A: Putative ketol-acid reductoisomerase (Os05g0573700 protein)
B: Putative ketol-acid reductoisomerase (Os05g0573700 protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8827
Polymers114,7602
Non-polymers1225
Water15,133840
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-54 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.032, 92.901, 91.187
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-418-

HOH

DetailsThe dimer within the asymmetric unit

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Components

#1: Protein Putative ketol-acid reductoisomerase (Os05g0573700 protein)


Mass: 57380.035 Da / Num. of mol.: 2 / Fragment: sequence database residues 54-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: ilvB, OJ1735_C10.18, Os05g0573700 / Plasmid: PET30(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q65XK0, ketol-acid reductoisomerase (NADP+)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.5 and 15% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 2000 / Details: Osmic Mirrors
RadiationMonochromator: Mirrors Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→40.4 Å / Num. all: 143459 / Num. obs: 143459 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.85 % / Rmerge(I) obs: 0.035 / Rsym value: 0.035
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.2 / Num. unique all: 10300 / Rsym value: 0.305 / % possible all: 69

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Processing

Software
NameVersionClassification
CrystalCleardata collection
EPMRphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YVE

1yve


Resolution: 1.55→37.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.115 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23017 7206 5 %RANDOM
Rwork0.20166 ---
obs0.20307 136249 96 %-
all-143459 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.02 Å2
2---0.09 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 5 840 8433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228122
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.96411057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.86751099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69324.39369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.291151457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4571549
X-RAY DIFFRACTIONr_chiral_restr0.0950.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026217
X-RAY DIFFRACTIONr_nbd_refined0.2120.24211
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2680
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.238
X-RAY DIFFRACTIONr_mcbond_it0.7341.55203
X-RAY DIFFRACTIONr_mcangle_it1.0928176
X-RAY DIFFRACTIONr_scbond_it1.8533305
X-RAY DIFFRACTIONr_scangle_it2.7414.52821
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.551 365 -
Rwork0.507 6938 -
obs--66.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7777-0.6330.29011.0258-0.31310.37590.05730.12190.13-0.0675-0.0486-0.04410.05560.0049-0.0086-0.0281-0.0215-0.0012-0.0681-0.0031-0.0761-53.1765.2228.868
20.58470.0543-0.12710.0605-0.07250.31930.00870.0030.11950.00040.0088-0.05470.00280.0267-0.0175-0.0079-0.00520.0154-0.08180.0050.0153-35.0461.90452.36
30.7518-0.1913-0.50090.5870.03670.8518-0.081-0.0293-0.08910.00990.0530.02250.06610.03380.0281-0.0166-0.01540.0051-0.06360.0008-0.0679-65.771-28.66976.125
40.36620.0454-0.09720.20280.05310.3666-0.0282-0.07260.07310.06160.0322-0.00230.02720.0426-0.0040.02010.0179-0.0097-0.0511-0.0187-0.0481-51.206-1.80676.604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 307
2X-RAY DIFFRACTION2A308 - 580
3X-RAY DIFFRACTION3B1086 - 1307
4X-RAY DIFFRACTION4B1308 - 1575

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