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- PDB-4rji: Acetolactate synthase from Bacillus subtilis bound to ThDP - crys... -

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Basic information

Entry
Database: PDB / ID: 4rji
TitleAcetolactate synthase from Bacillus subtilis bound to ThDP - crystal form I
ComponentsAcetolactate synthase
KeywordsLYASE / ThDP
Function / homologyThiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / THIAMINE DIPHOSPHATE / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSommer, B. / von Moeller, H. / Haack, M. / Qoura, F. / Langner, C. / Bourenkov, G. / Garbe, D. / Brueck, T. / Loll, B.
CitationJournal: Chembiochem / Year: 2015
Title: Detailed Structure-Function Correlations of Bacillus subtilis Acetolactate Synthase.
Authors: Sommer, B. / von Moeller, H. / Haack, M. / Qoura, F. / Langner, C. / Bourenkov, G. / Garbe, D. / Loll, B. / Bruck, T.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Database references
Revision 1.3Sep 20, 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_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_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
B: Acetolactate synthase
C: Acetolactate synthase
D: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,87613
Polymers255,8834
Non-polymers1,9939
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26270 Å2
ΔGint-129 kcal/mol
Surface area64690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.647, 140.647, 238.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Acetolactate synthase


Mass: 63970.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: PY79 / Gene: U712_18080 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: V5MX36, EC: 4.1.3.18
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 % (v/v) polyethylene glycol 300, 200 mM Ca acetate, 100 mM Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 19, 2012
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 40326 / Num. obs: 40142 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 53.6 Å2
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 7.1 % / % possible all: 98.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OZF

1ozf


Resolution: 3.2→29.664 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 2008 5.01 %RANDOM
Rwork0.1868 ---
obs0.1901 40118 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→29.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16850 0 121 23 16994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517289
X-RAY DIFFRACTIONf_angle_d0.88823516
X-RAY DIFFRACTIONf_dihedral_angle_d12.186380
X-RAY DIFFRACTIONf_chiral_restr0.0542698
X-RAY DIFFRACTIONf_plane_restr0.0053077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.27910.32921380.25232613X-RAY DIFFRACTION98
3.2791-3.36760.35311410.24832677X-RAY DIFFRACTION100
3.3676-3.46660.32271410.25382683X-RAY DIFFRACTION100
3.4666-3.57830.29441410.2322681X-RAY DIFFRACTION100
3.5783-3.70590.32141420.23992700X-RAY DIFFRACTION100
3.7059-3.8540.26441410.21512672X-RAY DIFFRACTION100
3.854-4.0290.3031430.21862717X-RAY DIFFRACTION100
4.029-4.24090.26711420.18832702X-RAY DIFFRACTION100
4.2409-4.50570.19161430.16432719X-RAY DIFFRACTION100
4.5057-4.85220.24391440.1522734X-RAY DIFFRACTION100
4.8522-5.3380.2171440.15732726X-RAY DIFFRACTION100
5.338-6.10450.23281450.16832764X-RAY DIFFRACTION100
6.1045-7.6690.20451480.16052807X-RAY DIFFRACTION100
7.669-29.66540.20831550.14592915X-RAY DIFFRACTION99

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