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- PDB-5wdg: Acetolactate Synthase from Klebsiella pneumoniae in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5wdg
TitleAcetolactate Synthase from Klebsiella pneumoniae in Complex with a Reaction Intermediate
ComponentsAcetolactate synthase, catabolic
KeywordsTRANSFERASE / Intermediate / Synthase / ThDP
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
Chem-A4Y / PHOSPHATE ION / PYRUVIC ACID / Acetolactate synthase, catabolic
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å
AuthorsLatta, A.J. / Andrews, F.H. / McLeish, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Acetolactate Synthase from Klebsiella pneumoniae in Complex with Mechanism-Based Inhibitor
Authors: Latta, A.J. / Andrews, F.H. / McLeish, M.J.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
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.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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,73914
Polymers125,1102
Non-polymers1,62912
Water8,935496
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)253,47828
Polymers250,2204
Non-polymers3,25824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19640 Å2
ΔGint-138 kcal/mol
Surface area69460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.470, 134.410, 110.745
Angle α, β, γ (deg.)90.000, 95.450, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-947-

HOH

21B-960-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 6 or (resid 7 and (name...
21(chain F and (resseq 6 or (resid 7 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 6 or (resid 7 and (name...A6
121(chain A and (resseq 6 or (resid 7 and (name...A7
131(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
141(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
151(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
161(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
171(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
181(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
191(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
1101(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
1111(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
1121(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
1131(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
1141(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
1151(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
1161(chain A and (resseq 6 or (resid 7 and (name...A6 - 554
211(chain F and (resseq 6 or (resid 7 and (name...F6
221(chain F and (resseq 6 or (resid 7 and (name...F7
231(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
241(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
251(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
261(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
271(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
281(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
291(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
2101(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
2111(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
2121(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
2131(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
2141(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
2151(chain F and (resseq 6 or (resid 7 and (name...F2 - 3
2161(chain F and (resseq 6 or (resid 7 and (name...F2 - 3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetolactate synthase, catabolic / ALS


Mass: 62555.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: budB, ilvK / Production host: Escherichia coli (E. coli) / References: UniProt: P27696, acetolactate synthase

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Non-polymers , 5 types, 508 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-A4Y / (2S,3S)-2,3-dihydroxy-3-[(7S,8R,9aS)-8-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2,7-dimethyl-5,7,8,10-tetrahydro-9aH-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-9a-yl]-2-methylbutanoic acid


Mass: 558.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H28N4O11P2S
#5: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M NaHEPES, 5-10% PEG8000, and 3-12% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.12→85.24 Å / Num. obs: 70789 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.082 / Rrim(I) all: 0.153 / Net I/σ(I): 6.5 / Num. measured all: 238251 / Scaling rejects: 53
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.12-2.161.1240.1890.7231.3499.7
10.15-85.240.0470.9940.0310.05797.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.88 Å55.12 Å
Translation7.88 Å55.12 Å

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Processing

Software
NameVersionClassification
MOSFLMdata processing
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZH

1ozh


Resolution: 2.12→55.122 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.42
RfactorNum. reflection% reflection
Rfree0.247 3528 4.99 %
Rwork0.2044 --
obs0.2065 70725 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 225.23 Å2 / Biso mean: 50.5091 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 2.12→55.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 148 496 8698
Biso mean--62.23 42.8 -
Num. residues----1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028310
X-RAY DIFFRACTIONf_angle_d0.61211348
X-RAY DIFFRACTIONf_chiral_restr0.0441307
X-RAY DIFFRACTIONf_plane_restr0.0031485
X-RAY DIFFRACTIONf_dihedral_angle_d11.1062932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5623X-RAY DIFFRACTION5.859TORSIONAL
12A5623X-RAY DIFFRACTION5.859TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.116-2.1450.40851560.35462661281799
2.145-2.17560.34881380.328526632801100
2.1756-2.20810.33341550.30227012856100
2.2081-2.24260.31611200.306326832803100
2.2426-2.27940.40281320.34382633276599
2.2794-2.31870.28621230.295627202843100
2.3187-2.36080.32591320.267727002832100
2.3608-2.40630.28861320.25826672799100
2.4063-2.45540.30581560.250926602816100
2.4554-2.50880.27181450.241126822827100
2.5088-2.56710.29661420.235227032845100
2.5671-2.63130.24951440.227526772821100
2.6313-2.70250.32141240.238427182842100
2.7025-2.7820.26851510.225326682819100
2.782-2.87180.29631430.217626692812100
2.8718-2.97440.24491340.221526842818100
2.9744-3.09350.27681360.215427102846100
3.0935-3.23430.26061740.212926612835100
3.2343-3.40480.24321600.203126872847100
3.4048-3.6180.23441400.181526762816100
3.618-3.89730.20861370.170127032840100
3.8973-4.28940.18621260.154527332859100
4.2894-4.90970.17711290.136527022831100
4.9097-6.18440.20351520.170227142866100
6.1844-55.14080.20611470.16712722286999

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