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- PDB-5ahk: Crystal structure of acetohydroxy acid synthase Pf5 from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 5ahk
TitleCrystal structure of acetohydroxy acid synthase Pf5 from Pseudomonas protegens
ComponentsACETOLACTATE SYNTHASE II, LARGE SUBUNIT
KeywordsTRANSFERASE / THIAMINE DIPHOSPHATE-DEPENDENT ENZYME / FAD-BINDING / CARBOLIGATION REACTION
Function / homology
Function and homology information


thiamine pyrophosphate binding / catalytic activity / nucleotide binding / magnesium ion binding
Similarity search - Function
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 ...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
FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Acetolactate synthase II, large subunit
Similarity search - Component
Biological speciesPSEUDOMONAS PROTEGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDobritzsch, D. / Loschonsky, S. / Mueller, M. / Schneider, G.
CitationJournal: To be Published
Title: The Crystal Structure of the Acetohydroxy Acid Synthase Pf5 from Pseudomonas Protegens
Authors: Dobritzsch, D. / Loschonsky, S. / Mueller, M. / Schneider, G.
History
DepositionFeb 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _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 II, LARGE SUBUNIT
B: ACETOLACTATE SYNTHASE II, LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3378
Polymers129,8662
Non-polymers2,4706
Water15,691871
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-85.5 kcal/mol
Surface area34730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.220, 139.870, 65.340
Angle α, β, γ (deg.)90.00, 97.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 565 / Label seq-ID: 21 - 585

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.1406, -0.01088, -0.99), (-0.004833, -0.9999, 0.0103), (-0.9901, 0.003336, -0.1407)
Vector: 9.88, -182.9, 12.81)

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Components

#1: Protein ACETOLACTATE SYNTHASE II, LARGE SUBUNIT / ACETOHYDROXY ACID SYNTHASE


Mass: 64933.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-TERMINALLY HIS-TAGGED / Source: (gene. exp.) PSEUDOMONAS PROTEGENS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K6F7, acetolactate synthase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHIS-TAG FUSED TO N-TERMINUS

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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: 2.28 Å3/Da / Density % sol: 46 % / Description: THE DATA ARE TWINNED
Crystal growpH: 6.5
Details: 10% (W/V) PEG 4000, 0.1 M MES/IMIDAZOLE PH 6.5, 0.3 M MGCL2, 0.3 M CACL2, 17% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.526
11L, -K, H20.474
ReflectionResolution: 1.55→49.2 Å / Num. obs: 151815 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / % possible all: 81.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YBH

1ybh


Resolution: 1.55→49.22 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.704 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 7732 5.1 %RANDOM
Rwork0.1511 ---
obs0.15227 144040 90.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.199 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å20 Å22.87 Å2
2--7.44 Å20 Å2
3----4.38 Å2
Refinement stepCycle: LAST / Resolution: 1.55→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8530 0 160 871 9561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199157
X-RAY DIFFRACTIONr_bond_other_d0.0040.028824
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.95812474
X-RAY DIFFRACTIONr_angle_other_deg1.011320334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38351190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36624.447398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.353151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9411555
X-RAY DIFFRACTIONr_chiral_restr0.0840.21405
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210856
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022091
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5510.9394507
X-RAY DIFFRACTIONr_mcbond_other0.5510.9384506
X-RAY DIFFRACTIONr_mcangle_it0.9291.4045652
X-RAY DIFFRACTIONr_mcangle_other0.9281.4055653
X-RAY DIFFRACTIONr_scbond_it0.6921.0384650
X-RAY DIFFRACTIONr_scbond_other0.6921.0384646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0941.5236774
X-RAY DIFFRACTIONr_long_range_B_refined3.1169.30242121
X-RAY DIFFRACTIONr_long_range_B_other2.9749.00541266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 35019 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 500 -
Rwork0.285 8837 -
obs--74.87 %
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)
10.5351-0.0850.04110.2806-0.09460.44930.0134-0.05-0.01630.0190.0066-0.01990.05290.0041-0.01990.0649-0.00440.00210.00510.00010.05960.2626-104.920527.4342
20.3897-0.09410.07890.267-0.12710.5245-0.02110.00440.0637-0.02220.00880.0057-0.0131-0.03330.01240.0388-0.00010.00060.0028-0.00430.087-16.2851-77.3848.3924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 703
2X-RAY DIFFRACTION2B1 - 703

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