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- PDB-5d6r: Acetolactate Synthase from Klebsiella pneumoniae in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5d6r
TitleAcetolactate Synthase from Klebsiella pneumoniae in Complex with Mechanism-Based Inhibitor
ComponentsAcetolactate synthase, catabolic
KeywordsTRANSFERASE / Inhibition Intermediate Synthase
Function / homology
Function and homology information


butanediol metabolic process / acetolactate synthase / acetolactate synthase activity / carboxylic acid metabolic process / thiamine pyrophosphate 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-EN0 / PHOSPHATE ION / Acetolactate synthase, catabolic
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.276 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
DepositionAug 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.3Sep 27, 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_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,55211
Polymers125,1102
Non-polymers1,4429
Water4,810267
1
B: Acetolactate synthase, catabolic
M: Acetolactate synthase, catabolic
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)253,10522
Polymers250,2204
Non-polymers2,88418
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20780 Å2
ΔGint-141 kcal/mol
Surface area68110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.120, 133.350, 110.624
Angle α, β, γ (deg.)90.000, 95.400, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21chain M

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALSERSERchain BBA7 - 55627 - 576
2HISHISHISHISchain MMB020

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Components

#1: Protein Acetolactate synthase, catabolic / ALS


Mass: 62555.113 Da / Num. of mol.: 2 / Mutation: T407S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: budB, ilvK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27696, acetolactate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / 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-EN0 / 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-[(Z)-2-fluoro-1-hydroxy-2-phosphonoethenyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium


Mass: 565.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21FN4O11P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Sodium HEPES, 5-10% PEG 8000, 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
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.276→55.07 Å / Num. obs: 56232 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 38.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Net I/σ(I): 8.5 / Num. measured all: 196557 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.276-2.340.9761.41565146230.3450.62699.8
9.66-55.070.0212926117590.9990.01398.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.7data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OZF

1ozf


Resolution: 2.276→55.066 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1999 3.56 %
Rwork0.2005 54173 -
obs0.2018 56172 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.72 Å2 / Biso mean: 53.996 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.276→55.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8188 0 83 267 8538
Biso mean--53.74 43.96 -
Num. residues----1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038425
X-RAY DIFFRACTIONf_angle_d0.68211493
X-RAY DIFFRACTIONf_chiral_restr0.0271313
X-RAY DIFFRACTIONf_plane_restr0.0031508
X-RAY DIFFRACTIONf_dihedral_angle_d11.8982989
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B5921X-RAY DIFFRACTION6.19TORSIONAL
12M5921X-RAY DIFFRACTION6.19TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.276-2.33290.3661420.35243835397799
2.3329-2.3960.38121430.342938614004100
2.396-2.46650.34261430.316438974040100
2.4665-2.54610.34441420.285938163958100
2.5461-2.63710.28611430.272438624005100
2.6371-2.74270.30151420.258338674009100
2.7427-2.86750.2891420.238138483990100
2.8675-3.01870.24711420.228638584000100
3.0187-3.20780.30071430.22838654008100
3.2078-3.45550.24461440.204138864030100
3.4555-3.80310.19861420.176938754017100
3.8031-4.35330.18221430.148738714014100
4.3533-5.48390.17831440.14339084052100
5.4839-55.08250.18921440.15333924406899
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)
12.1137-0.4367-0.29332.04960.41492.08320.1411-0.40940.32210.15080.2427-0.36260.05260.5539-0.2670.29120.001-0.03290.4057-0.13040.375215.317225.031.0303
21.1407-0.0155-1.02861.3494-0.55642.28910.17390.29810.3612-0.32740.30750.190.0437-0.1672-0.23410.3852-0.0177-0.0180.4130.15640.4617.839530.2183-27.8074
30.27990.0726-0.68870.5862-0.32991.83920.66480.39320.705-0.32120.18440.1592-0.9018-0.6898-0.17290.71580.12080.38060.41960.35170.9619-4.765147.52-15.3679
41.9975-0.1651-0.11761.62370.09621.2775-0.141-0.23140.09520.2130.1314-0.0878-0.01710.0709-0.01620.36210.0697-0.05940.3882-0.00030.28473.3541-4.716216.5292
53.38331.537-0.17061.68780.26131.2604-0.11290.48570.6090.06760.20860.56410.1177-0.2935-0.01630.3594-0.06790.00530.49420.10170.5086-29.0855-2.163214.9467
62.69050.3942-0.70941.53430.37241.31730.03080.01140.2908-0.0335-0.00670.48660.0959-0.36390.00420.3803-0.1456-0.06410.63950.14170.4706-32.7224-10.225410.8288
72.12820.07450.74511.02540.06411.5162-0.0268-0.2748-0.30010.02190.09890.11150.4324-0.402-0.07830.4071-0.12010.00830.40430.05950.3471-14.9338-25.16163.2003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 7 through 173 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 174 through 463 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 464 through 556 )B0
4X-RAY DIFFRACTION4chain 'M' and (resid -4 through 173 )M0
5X-RAY DIFFRACTION5chain 'M' and (resid 174 through 304 )M0
6X-RAY DIFFRACTION6chain 'M' and (resid 305 through 383 )M0
7X-RAY DIFFRACTION7chain 'M' and (resid 384 through 554 )M0

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