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- PDB-4bt6: acetolactate decarboxylase with a bound glycerol -

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Basic information

Entry
Database: PDB / ID: 4bt6
Titleacetolactate decarboxylase with a bound glycerol
ComponentsALPHA-ACETOLACTATE DECARBOXYLASE
KeywordsLYASE / ACETOIN BIOSYNTHESIS / STEREOSELECTIVE DECARBOXYLATION / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


acetolactate decarboxylase / acetoin biosynthetic process / acetolactate decarboxylase activity
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 speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsA Marlow, V. / Rea, D. / Najmudin, S. / Wills, M. / Fulop, V.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Structure and Mechanism of Acetolactate Decarboxylase.
Authors: Marlow, V.A. / Rea, D. / Najmudin, S. / Wills, M. / Fulop, V.
History
DepositionJun 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source / _diffrn_source.type
Revision 1.3Dec 20, 2023Group: 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 / pdbx_struct_special_symmetry / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-ACETOLACTATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2646
Polymers28,8311
Non-polymers4345
Water5,909328
1
A: ALPHA-ACETOLACTATE DECARBOXYLASE
hetero molecules

A: ALPHA-ACETOLACTATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52912
Polymers57,6612
Non-polymers86810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area4130 Å2
ΔGint-87.7 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.130, 47.130, 198.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2035-

HOH

21A-2060-

HOH

31A-2113-

HOH

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Components

#1: Protein ALPHA-ACETOLACTATE DECARBOXYLASE / ALDC / ACETOLACTATE DECARBOXYLASE


Mass: 28830.621 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BREVIBACILLUS BREVIS (bacteria) / Plasmid: PJA199 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): JA222 / Variant (production host): TOC46 / References: UniProt: P23616, acetolactate decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M TRIMETHYLAMINE N-OXIDE (TMAO), 0.1 M TRIS PH 8.5, 28-33 PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 18, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→41 Å / Num. obs: 34655 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 14.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 3.4 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BT2

4bt2


Resolution: 1.6→40.82 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.31 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21222 1386 4 %RANDOM
Rwork0.17045 ---
obs0.17212 33269 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 25 328 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221951
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9662634
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20925.76192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72515344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.302154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211452
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5971.51181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26421922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5283770
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2944.5712
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
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 90 -
Rwork0.379 2140 -
obs--88 %
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)
10.5390.0655-0.09140.24620.16240.86950.0001-0.0066-0.02340.01510.00090.01420.0435-0.0577-0.0010.0733-0.0146-0.00110.0910.00120.0075-22.80224.21179.76
20.4029-0.03650.16890.17670.17760.8731-0.0131-0.00470.06930.00940.0207-0.0072-0.08390.0218-0.00760.0936-0.02-0.0080.08310.00850.0162-11.40936.18585.962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 100
2X-RAY DIFFRACTION1A146 - 165
3X-RAY DIFFRACTION1A224 - 244
4X-RAY DIFFRACTION2A101 - 145
5X-RAY DIFFRACTION2A166 - 223
6X-RAY DIFFRACTION2A245 - 256

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