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

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Basic information

Entry
Database: PDB / ID: 4rjj
TitleAcetolactate synthase from Bacillus subtilis bound to ThDP - crystal form II
ComponentsAcetolactate synthase
KeywordsLYASE / ThDP
Function / homologyThiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / THIAMINE DIPHOSPHATE / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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
E: Acetolactate synthase
F: Acetolactate synthase
G: Acetolactate synthase
H: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,36557
Polymers497,4948
Non-polymers9,87149
Water35,2191955
1
A: Acetolactate synthase
B: Acetolactate synthase
C: Acetolactate synthase
D: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,90630
Polymers248,7474
Non-polymers5,15926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31300 Å2
ΔGint-70 kcal/mol
Surface area65690 Å2
MethodPISA
2
E: Acetolactate synthase
F: Acetolactate synthase
hetero molecules

E: Acetolactate synthase
F: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,65328
Polymers248,7474
Non-polymers4,90624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area31010 Å2
ΔGint-63 kcal/mol
Surface area65650 Å2
MethodPISA
3
G: Acetolactate synthase
H: Acetolactate synthase
hetero molecules

G: Acetolactate synthase
H: Acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,26526
Polymers248,7474
Non-polymers4,51822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area31730 Å2
ΔGint-65 kcal/mol
Surface area64640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.671, 170.003, 339.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11E-833-

HOH

21G-906-

HOH

31H-774-

HOH

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Acetolactate synthase


Mass: 62186.750 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: PY79 / Gene: U712_18080 / Plasmid: pCBR / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: V5MX36, EC: 4.1.3.18

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Non-polymers , 5 types, 2004 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1955 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 45 % (v/v) PEG 200, 100 mM Tris/HCl, pH 7.0, 50 mM Li2SO4, 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: Apr 17, 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: 2.34→48.437 Å / Num. obs: 268024 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 27.5 Å2
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 4.1 % / % possible all: 94.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→30 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 13394 5 %RANDOM
Rwork0.1715 ---
obs0.1737 267826 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33929 0 605 1955 36489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935334
X-RAY DIFFRACTIONf_angle_d1.17747964
X-RAY DIFFRACTIONf_dihedral_angle_d14.97613245
X-RAY DIFFRACTIONf_chiral_restr0.0755470
X-RAY DIFFRACTIONf_plane_restr0.0066242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.36560.29693880.23317365X-RAY DIFFRACTION86
2.3656-2.39340.27334140.22637859X-RAY DIFFRACTION92
2.3934-2.42260.29974280.22658142X-RAY DIFFRACTION95
2.4226-2.45330.27964440.22048433X-RAY DIFFRACTION100
2.4533-2.48550.26854510.2118587X-RAY DIFFRACTION100
2.4855-2.51960.24774470.19888481X-RAY DIFFRACTION100
2.5196-2.55560.26984490.19838531X-RAY DIFFRACTION100
2.5556-2.59370.24624490.18838539X-RAY DIFFRACTION100
2.5937-2.63420.25514480.19078496X-RAY DIFFRACTION100
2.6342-2.67740.2534510.19248572X-RAY DIFFRACTION100
2.6774-2.72360.24924500.18738558X-RAY DIFFRACTION100
2.7236-2.77310.24834460.18868480X-RAY DIFFRACTION100
2.7731-2.82640.25454510.18578555X-RAY DIFFRACTION100
2.8264-2.88410.24224500.18568548X-RAY DIFFRACTION100
2.8841-2.94680.25174510.18878577X-RAY DIFFRACTION100
2.9468-3.01540.24294470.18778482X-RAY DIFFRACTION99
3.0154-3.09080.23814500.18758558X-RAY DIFFRACTION100
3.0908-3.17430.244490.18368536X-RAY DIFFRACTION100
3.1743-3.26770.2184510.17798560X-RAY DIFFRACTION99
3.2677-3.37320.22984480.17928507X-RAY DIFFRACTION99
3.3732-3.49370.21624500.17328564X-RAY DIFFRACTION99
3.4937-3.63350.22474500.16838546X-RAY DIFFRACTION99
3.6335-3.79880.18734500.15678548X-RAY DIFFRACTION99
3.7988-3.9990.17344510.14638567X-RAY DIFFRACTION99
3.999-4.24940.19084510.14338568X-RAY DIFFRACTION99
4.2494-4.57730.16974510.13538555X-RAY DIFFRACTION99
4.5773-5.03750.16964520.13658597X-RAY DIFFRACTION99
5.0375-5.76540.18354550.15778641X-RAY DIFFRACTION99
5.7654-7.25990.20114590.17278722X-RAY DIFFRACTION99
7.2599-48.4470.16854630.14798758X-RAY DIFFRACTION96

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