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- PDB-6j3d: Crystal structure of acetolactate decarboxylase from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 6j3d
TitleCrystal structure of acetolactate decarboxylase from Bacillus subtilis subspecies spizizenii in space group P21212
ComponentsAlpha-acetolactate decarboxylase
KeywordsLYASE / enzyme / decarboxylase
Function / homology
Function and homology information


acetolactate decarboxylase / acetoin biosynthetic process / acetolactate decarboxylase activity / metal ion binding
Similarity search - Function
Alpha-acetolactate decarboxylase / Alpha-acetolactate decarboxylase / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-acetolactate decarboxylase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYoon, S.I.
CitationJournal: Korean J Microbiol. / Year: 2019
Title: Crystal structure of alpha-acetolactate decarboxylase from Bacillus subtilis subspecies spizizeni.
Authors: Eom, J. / Oh, H.B. / Yoon, S.I.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Nov 22, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-acetolactate decarboxylase
B: Alpha-acetolactate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7484
Polymers58,6182
Non-polymers1312
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-87 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.276, 129.643, 45.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 300
2116B1 - 300

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Components

#1: Protein Alpha-acetolactate decarboxylase


Mass: 29308.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (strain ATCC 23059 / NRRL B-14472 / W23) (bacteria)
Strain: ATCC 23059 / NRRL B-14472 / W23 / Gene: alsD, BSUW23_17695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0U503, acetolactate decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 4000, 0.08M ammonium sulfate, 0.1M sodium acetate, pH 4.5, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 58087 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 44.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 2833 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4BT4

4bt4


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.303 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19137 2922 5.1 %RANDOM
Rwork0.17141 ---
obs0.17242 54766 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 21.599 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 2 334 3988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223773
X-RAY DIFFRACTIONr_bond_other_d0.0010.022495
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9525129
X-RAY DIFFRACTIONr_angle_other_deg0.88436090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83824.759187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26515603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9531516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
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_it0.9131.52329
X-RAY DIFFRACTIONr_mcbond_other0.2961.5950
X-RAY DIFFRACTIONr_mcangle_it1.62923781
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.73331444
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2434.51343
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2975 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.315
loose thermal1.8810
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 224 -
Rwork0.243 3952 -
obs--99.69 %
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)
10.5964-0.31040.1891.65950.52551.2889-0.00230.0068-0.02660.05120.0496-0.13880.00920.0803-0.04730.23770.0212-0.02480.0122-0.01590.0686-11.12528.889-14.457
20.6539-0.13510.21081.4028-0.0150.99420.0162-0.00920.03090.07260.03850.0320.01190.0987-0.05470.21920.015-0.00420.0149-0.01260.0295-24.63959.594-9.632
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 252
2X-RAY DIFFRACTION2B20 - 251

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