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- PDB-3fr8: rice Ketolacid reductoisomerase in complex with Mg2+-NADPH -

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Basic information

Entry
Database: PDB / ID: 3fr8
Titlerice Ketolacid reductoisomerase in complex with Mg2+-NADPH
ComponentsPutative ketol-acid reductoisomerase (Os05g0573700 protein)
KeywordsOXIDOREDUCTASE / Rossmann fold / Branched-chain amino acid biosynthesis / Knotted protein / NADPH / 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
Chem-NDP / DI(HYDROXYETHYL)ETHER / Ketol-acid reductoisomerase, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLeung, E.W.W. / Guddat, L.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 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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_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.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_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)116,88010
Polymers114,7602
Non-polymers2,1208
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-76 kcal/mol
Surface area35290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.060, 162.060, 196.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-24-

HOH

DetailsThe dimer within the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#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+)

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Non-polymers , 6 types, 178 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS-HCl pH 8.5, 1M (NH4)2SO4, 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 SATURN 944 / Detector: CCD / Date: Aug 1, 2008 / 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: 2.8→19.22 Å / Num. all: 31711 / Num. obs: 31711 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 2 / Num. unique all: 3170 / Rsym value: 0.354 / % possible all: 99.8

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Processing

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

1yve


Resolution: 2.8→19.22 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.885 / SU B: 32.777 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.424 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28398 1598 5.1 %RANDOM
Rwork0.23307 ---
obs0.23564 29991 97.71 %-
all-31711 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.985 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7815 0 112 170 8097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228090
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.97610954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01251020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60924.176352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.385151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3611548
X-RAY DIFFRACTIONr_chiral_restr0.0750.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026109
X-RAY DIFFRACTIONr_nbd_refined0.190.24227
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2343
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.27
X-RAY DIFFRACTIONr_mcbond_it0.2111.55168
X-RAY DIFFRACTIONr_mcangle_it0.37428077
X-RAY DIFFRACTIONr_scbond_it0.40833291
X-RAY DIFFRACTIONr_scangle_it0.7094.52876
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 118 -
Rwork0.318 2157 -
obs--99.17 %
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)
12.9994-0.00670.06183.66480.69162.94420.01930.11390.525-0.16130.0182-0.67060.0420.2577-0.0375-0.2679-0.08740.1707-0.3372-0.07370.004924.700229.728748.7329
20.9516-0.13710.18432.19170.23751.5146-0.0727-0.15540.0819-0.00870.0912-0.15750.1568-0.1859-0.0186-0.172-0.05440.0188-0.1168-0.0617-0.1564-0.505920.393160.5855
31.8941-0.8747-0.27286.28586.617810.86880.12980.08850.2408-0.1013-0.42870.0016-0.2323-1.27440.2989-0.13610.0911-0.0782-0.0346-0.1522-0.1109-15.789262.909171.0865
41.65420.06690.53931.28240.45222.1581-0.2352-0.61150.29180.32610.02-0.0118-0.0485-0.60990.2153-0.13690.1353-0.08460.1106-0.2569-0.1205-7.773238.375182.2249
5121.594914.113212.812424.0518-1.83671.84290.6942.39010.36540.39060.31831.498-1.3179-2.899-1.01240.0080.0575-0.0118-0.0015-0.1655-0.0219-28.655243.995974.3514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA81 - 30610 - 235
2X-RAY DIFFRACTION2AA307 - 581236 - 510
3X-RAY DIFFRACTION3BB77 - 3066 - 235
4X-RAY DIFFRACTION4BB307 - 581236 - 510
5X-RAY DIFFRACTION5BB582 - 593511 - 522

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