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- PDB-1bfd: BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA -

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Basic information

Entry
Database: PDB / ID: 1bfd
TitleBENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
ComponentsBENZOYLFORMATE DECARBOXYLASE
KeywordsLYASE / CARBON-CARBON / DECARBOXYLASE / MANDELATE CATABOLISM / THIAMIN DIPHOSPHATE
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / acetolactate synthase activity / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / 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 ...Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / 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
THIAMINE DIPHOSPHATE / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.6 Å
AuthorsHasson, M.S. / Muscate, A. / Mcleish, M.J. / Polovnikova, L.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1998
Title: The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
Authors: Hasson, M.S. / Muscate, A. / McLeish, M.J. / Polovnikova, L.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D.
#1: Journal: Protein Sci. / Year: 1995
Title: Purification and Crystallization of Benzoylformate Decarboxylase
Authors: Hasson, M.S. / Muscate, A. / Henehan, G.T. / Guidinger, P.F. / Petsko, G.A. / Ringe, D. / Kenyon, G.L.
History
DepositionApr 30, 1998Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9335
Polymers56,4031
Non-polymers5304
Water6,233346
1
A: BENZOYLFORMATE DECARBOXYLASE
hetero molecules

A: BENZOYLFORMATE DECARBOXYLASE
hetero molecules

A: BENZOYLFORMATE DECARBOXYLASE
hetero molecules

A: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,73020
Polymers225,6114
Non-polymers2,11916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area26700 Å2
ΔGint-231 kcal/mol
Surface area59380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.300, 96.600, 138.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-531-

MG

21A-792-

HOH

31A-798-

HOH

41A-803-

HOH

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Components

#1: Protein BENZOYLFORMATE DECARBOXYLASE


Mass: 56402.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: RF4738 / Gene: MDLC / Plasmid: PKK233-2 / Gene (production host): MDLC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.44 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 22% (V/V) POLYETHYLENE GLYCOL WITH AN AVERAGE MOLECULAR WEIGHT OF 400 KDA (PEG 400), 0.15 M ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 22% (V/V) POLYETHYLENE GLYCOL WITH AN AVERAGE MOLECULAR WEIGHT OF 400 KDA (PEG 400), 0.15 M CACL2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5). DROPS CONTAINED EQUAL VOLUMES (2 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [10 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 25 MM NAHEPES (PH 7.0)]., vapor diffusion - hanging drop
PH range: 7.0-8.5 / Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 mM1dropMgCl2
30.2 mMThDP1drop
425 mMNaHepes1drop
522 %(v/v)PEG4001reservoir
60.15 M1reservoirCaCl2
70.5 %MPD1reservoir
80.1 MTrisCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 59179 / % possible obs: 81 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 2.2 / % possible all: 32
Reflection
*PLUS
Num. measured all: 217078
Reflection shell
*PLUS
% possible obs: 32 %

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Processing

Software
NameVersionClassification
PROTSYSmodel building
X-PLOR3refinement
PROCESSdata reduction
MOSFLMdata reduction
RIGAKUdata scaling
PROTSYSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→5 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: VAL 524 IS THE LAST RESIDUE FOR WHICH INTERPRETABLE ELECTRON DENSITY WAS PRESENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2817 5 %RANDOM
Rwork0.152 ---
obs0.152 56642 80.6 %-
Displacement parametersBiso mean: 18.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 29 346 4303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.041.5
X-RAY DIFFRACTIONx_mcangle_it1.532
X-RAY DIFFRACTIONx_scbond_it2.312
X-RAY DIFFRACTIONx_scangle_it3.622.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 179 4.9 %
Rwork0.275 3497 -
obs--31.6 %
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 59179 / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44
LS refinement shell
*PLUS
Rfactor obs: 0.275

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