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- PDB-1ozg: The crystal structure of Klebsiella pneumoniae acetolactate synth... -

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Basic information

Entry
Database: PDB / ID: 1ozg
TitleThe crystal structure of Klebsiella pneumoniae acetolactate synthase with enzyme-bound cofactor and with an unusual intermediate
ComponentsAcetolactate synthase, catabolic
KeywordsLYASE / acetolactate synthase / acetohydroxyacid synthase / thiamin diphosphate
Function / homology
Function and homology information


butanediol metabolic process / acetolactate synthase complex / acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Acetolactate synthase, catabolic / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain ...Acetolactate synthase, catabolic / Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-HYDROXYETHYL DIHYDROTHIACHROME DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Acetolactate synthase, catabolic
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPang, S.S. / Duggleby, R.G. / Schowen, R.L. / Guddat, L.W.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Crystal Structures of Klebsiella pneumoniae Acetolactate Synthase with Enzyme-bound Cofactor and with an Unusual Intermediate.
Authors: Pang, S.S. / Duggleby, R.G. / Schowen, R.L. / Guddat, L.W.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_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_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.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_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_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
A: Acetolactate synthase, catabolic
B: Acetolactate synthase, catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,73616
Polymers122,7122
Non-polymers2,02414
Water11,025612
1
A: Acetolactate synthase, catabolic
B: Acetolactate synthase, catabolic
hetero molecules

A: Acetolactate synthase, catabolic
B: Acetolactate synthase, catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,47232
Polymers245,4234
Non-polymers4,04828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area27020 Å2
ΔGint-121 kcal/mol
Surface area68870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.488, 160.561, 129.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: -X,Y,-Z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetolactate synthase, catabolic / ALS


Mass: 61355.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: BUDB OR ILVK / Plasmid: pET30a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27696, EC: 4.1.3.18

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Non-polymers , 5 types, 626 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HE3 / 2-HYDROXYETHYL DIHYDROTHIACHROME DIPHOSPHATE / 2-{(9AS)-9A-[(1S)-1-HYDROXYETHYL]-2,7-DIMETHYL-9A,10-DIHYDRO-5H-PYRIMIDO[4,5-D][1,3]THIAZOLO[3,2-A]PYRIMIDIN-8-YL}ETHYL TRIHYDROGEN DIPHOSPHATE


Mass: 468.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N4O8P2S
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.42 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 8000, ethylene glycol, sodium HEPES , pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlenzyme1drop
250 mMpotassium phosphate1droppH7.0
31 mMThDP1drop
41 mM1dropMgCl2
51 mMdithiothreitol1drop
60.1 Msodium HEPES1reservoirpH7.5-7.7
76-8 %(w/v)PEG80001reservoir
86-9 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2002 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 48466 / Num. obs: 48466 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.057 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 3030 / Rsym value: 0.126 / % possible all: 49.3
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 170273 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 49.3 % / Num. unique obs: 3030 / Num. measured obs: 5047 / Rmerge(I) obs: 0.126

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Processing

Software
NameVersionClassification
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JSC

1jsc


Resolution: 2.3→100 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4836 -RANDOM
Rwork0.162 ---
all0.167 47977 --
obs0.167 47977 87.9 %-
Displacement parametersBiso mean: 26.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.284 Å20 Å20 Å2
2--4.492 Å20 Å2
3---0.792 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8256 0 126 612 8994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.23
X-RAY DIFFRACTIONc_dihedral_angle_d22.44
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.236 292 -
Rwork0.196 --
obs-2777 51.9 %
Refinement
*PLUS
Lowest resolution: 100 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.44
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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