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- PDB-3ulk: E. coli Ketol-acid reductoisomerase in complex with NADPH and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 3ulk
TitleE. coli Ketol-acid reductoisomerase in complex with NADPH and Mg2+
ComponentsKetol-acid reductoisomerase
KeywordsOXIDOREDUCTASE / Branched-chain amino acid biosynthesis / Rossmann fold / reductoisomerase / Acetolactate
Function / homology
Function and homology information


2-dehydropantoate 2-reductase activity / ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / pantothenate biosynthetic process / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
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. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...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. / 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 / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWong, S.H. / Lonhienne, T.G.A. / Winzor, D.J. / Schenk, G. / Guddat, L.W.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Bacterial and plant ketol-acid reductoisomerases have different mechanisms of induced fit during the catalytic cycle
Authors: Wong, S.H. / Lonhienne, T.G.A. / Winzor, D.J. / Schenk, G. / Guddat, L.W.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 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 / 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.pdbx_leaving_atom_flag / _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: Ketol-acid reductoisomerase
B: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,74417
Polymers108,2922
Non-polymers2,45315
Water13,872770
1
A: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules

B: Ketol-acid reductoisomerase
hetero molecules

B: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,48934
Polymers216,5834
Non-polymers4,90530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area15020 Å2
ΔGint-278 kcal/mol
Surface area71020 Å2
MethodPISA
2
B: Ketol-acid reductoisomerase
hetero molecules

B: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,48934
Polymers216,5834
Non-polymers4,90530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Unit cell
Length a, b, c (Å)144.459, 144.459, 217.545
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 54145.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ilvC / Production host: Escherichia coli (E. coli)
References: UniProt: P05793, ketol-acid reductoisomerase (NADP+)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M LiSO4, 0.1M Tris, 15% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 15, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→36.2 Å / Num. all: 59991 / Num. obs: 59991 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 27.41 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 57.2
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 12.1 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yrl

1yrl


Resolution: 2.3→36.15 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7921 / SU ML: 0.34 / Cross valid method: R-free / σ(F): 1.33 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 3011 5.06 %Random
Rwork0.1744 ---
all0.1802 59548 --
obs0.1774 59548 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.921 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 198.26 Å2 / Biso mean: 29.8796 Å2 / Biso min: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.2515 Å2-0 Å20 Å2
2---0.2515 Å2-0 Å2
3---0.5031 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7558 0 145 770 8473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078064
X-RAY DIFFRACTIONf_angle_d1.0910935
X-RAY DIFFRACTIONf_chiral_restr0.0731182
X-RAY DIFFRACTIONf_plane_restr0.0041426
X-RAY DIFFRACTIONf_dihedral_angle_d16.0083065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3003-2.33630.2821350.19882489262498
2.3363-2.37450.281210.183525432664100
2.3745-2.41550.31191190.214125542673100
2.4155-2.45940.36361240.20892518264299
2.4594-2.50670.29351420.20132517265999
2.5067-2.55780.30461480.19752503265199
2.5578-2.61340.29581400.18992542268299
2.6134-2.67420.25991590.19342521268099
2.6742-2.74110.28921380.19222514265299
2.7411-2.81520.29091450.212507265299
2.8152-2.8980.29241070.19642581268899
2.898-2.99150.28191470.1992536268399
2.9915-3.09830.2651510.19482536268799
3.0983-3.22230.23991370.189425672704100
3.2223-3.36890.24291300.186425852715100
3.3689-3.54630.25161250.186525902715100
3.5463-3.76830.23951350.165825992734100
3.7683-4.05890.19291460.15242571271799
4.0589-4.46670.16731210.12312613273499
4.4667-5.11150.17171380.12032640277899
5.1115-6.4340.19091430.17426822825100
6.434-36.15470.18281600.17442829298999
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)
10.03370.03540.05070.03880.0510.07360.0210.0176-0.0011-0.0280.0928-0.0985-0.01380.10150.04990.0737-0.0951-0.0460.2962-0.00720.165525.999542.489280.9497
20.0109-0.02370.02590.1048-0.0660.0674-0.0652-0.0315-0.0531-0.04950.069-0.0187-0.0257-0.0274-0.00430.1428-0.02930.06560.26930.04820.184321.223946.854958.5734
30.0053-0.0052-0.00210.00520.00220.0034-0.00320.0277-0.0016-0.04460.02470.0076-0.01220.0169-0.00280.1663-0.0928-0.04220.24390.02830.11669.866244.111552.6708
40.1246-0.0893-0.04090.39440.11720.04520.01640.0278-0.0159-0.10540.0727-0.02870.0147-0.0352-0.03810.13480.0021-0.00750.2412-0.0230.087714.431134.935960.7218
50.13960.0189-0.07390.0105-0.01890.11320.06370.01210.0248-0.0190.02140.00660.03630.0179-0.05620.09990.0364-0.00240.2733-0.030.164519.184433.199770.3313
60.20.11720.14920.17350.01350.16820.0493-0.0685-0.059-0.00810.0193-0.0736-0.05770.16870.03840.0849-0.01570.05870.15390.00720.118321.504748.983269.4933
70.00280.01570.00430.0608-0.00250.0094-0.0701-0.00090.0849-0.1024-0.02160.0593-0.0404-0.018-0.030.0944-0.0437-0.05840.2788-0.07130.197.100258.003882.3038
80.1582-0.06730.05720.0689-0.05650.06490.0093-0.04520.06170.0206-0.0305-0.03940.03120.00840.00510.069-0.0569-0.0210.2405-0.02240.10686.254254.718997.2932
90.01950.00730.00750.00230.00240.0003-0.00040.00170.0003-0.0097-0.07410.05130.0078-0.0757-0.03060.0204-0.0313-0.08290.2137-0.0810.2105-5.521952.020581.517
100.0199-0.0281-0.00090.05480.00210.01040.01090.02060.0394-0.0284-0.0669-0.0134-0.01820.0106-0.00490.0444-0.0584-0.04760.3034-0.05740.12455.494353.549584.4941
110.0058-0.00850.00490.0430.0110.0785-0.05350.04850.00770.0056-0.09140.0117-0.04530.02-0.01970.0595-0.0746-0.03370.2454-0.0690.16711.77167.132393.2129
120.11160.0804-0.04580.0891-0.01560.07520.04710.1288-0.01890.05030.0711-0.02250.04050.04440.05670.09250.0504-0.07050.1538-0.02060.085718.931343.1693168.6766
130.1269-0.0485-0.03030.1187-0.01770.08810.0223-0.0321-0.01760.0106-0.00960.07030.01270.01010.00790.13660.0257-0.01690.0747-0.01640.10373.364457.6719189.0945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 1:32)A1 - 32
2X-RAY DIFFRACTION2chain A and (resseq 33:58)A33 - 58
3X-RAY DIFFRACTION3chain A and (resseq 59:87)A59 - 87
4X-RAY DIFFRACTION4chain A and (resseq 88:121)A88 - 121
5X-RAY DIFFRACTION5chain A and (resseq 122:147)A122 - 147
6X-RAY DIFFRACTION6chain A and (resseq 148:186)A148 - 186
7X-RAY DIFFRACTION7chain A and (resseq 187:278)A187 - 278
8X-RAY DIFFRACTION8chain A and (resseq 279:309)A279 - 309
9X-RAY DIFFRACTION9chain A and (resseq 310:358)A310 - 358
10X-RAY DIFFRACTION10chain A and (resseq 359:431)A359 - 431
11X-RAY DIFFRACTION11chain A and (resseq 432:489)A432 - 489
12X-RAY DIFFRACTION12chain B and (resseq 1:226)B1 - 226
13X-RAY DIFFRACTION13chain B and (resseq 227:489)B227 - 489

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