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- PDB-5dei: BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA -

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Basic information

Entry
Database: PDB / ID: 5dei
TitleBENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / BENZOYLFORMATE DECARBOXYLASE / THIAMIN DIPHOSPHATE / BICARBONATE
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / thiamine pyrophosphate 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
BICARBONATE ION / THIAMINE DIPHOSPHATE / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBera, A.K. / Hasson, M.S.
Citation
Journal: to be published
Title: BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
Authors: Bera, A.K. / Hasson, M.S.
#1: Journal: J.Am.Chem.Soc. / Year: 2007
Title: Mechanism-based inactivation of benzoylformate decarboxylase, a thiamin diphosphate-dependent enzyme.
Authors: Bera, A.K. / Polovnikova, L.S. / Roestamadji, J. / Widlanski, T.S. / Kenyon, G.L. / McLeish, M.J. / Hasson, M.S.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
B: Benzoylformate decarboxylase
C: Benzoylformate decarboxylase
D: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,16526
Polymers223,7844
Non-polymers2,38022
Water42,3892353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28720 Å2
ΔGint-251 kcal/mol
Surface area58820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.166, 92.451, 93.715
Angle α, β, γ (deg.)63.590, 72.420, 72.880
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Benzoylformate decarboxylase / / BFDC


Mass: 55946.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: RF4738 / Gene: mdlC / Plasmid: PREP7 / Production host: Escherichia coli (E. coli) / References: UniProt: P20906, benzoylformate decarboxylase

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Non-polymers , 5 types, 2375 molecules

#2: Chemical
ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


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


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2353 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 293 K / Method: 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)
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→82 Å / Num. obs: 418656 / % possible obs: 86.22 % / Redundancy: 1 % / Biso Wilson estimate: 13.65 Å2 / Rmerge(I) obs: 0.44 / Net I/σ(I): 1.97
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 67.4 / % possible all: 44.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFD

1bfd


Resolution: 1.3→27.413 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1481 10017 2.39 %
Rwork0.1361 408639 -
obs0.1364 418656 86.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.74 Å2 / Biso mean: 19.4061 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 1.3→27.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15736 0 218 2353 18307
Biso mean--14.34 31.28 -
Num. residues----2096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916416
X-RAY DIFFRACTIONf_angle_d1.40222429
X-RAY DIFFRACTIONf_chiral_restr0.112507
X-RAY DIFFRACTIONf_plane_restr0.0092975
X-RAY DIFFRACTIONf_dihedral_angle_d13.9456053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3004-1.31510.23021550.23085899605437
1.3151-1.33060.24431790.22087723790249
1.3306-1.34680.27561990.22058668886755
1.3468-1.36390.21872350.21869603983861
1.3639-1.38180.22742750.2201105271080267
1.3818-1.40080.23172770.2109115601183773
1.4008-1.42080.21832910.2029124171270879
1.4208-1.4420.21893250.1999131131343883
1.442-1.46450.2153380.1918138131415187
1.4645-1.48850.19593480.1826141981454690
1.4885-1.51420.19353590.1717145221488192
1.5142-1.54170.17283580.1652147511510993
1.5417-1.57140.15753610.1534148001516194
1.5714-1.60340.17313680.1506149101527894
1.6034-1.63830.15413680.1443150281539695
1.6383-1.67640.16193640.1431150081537295
1.6764-1.71830.16153590.1411150471540695
1.7183-1.76480.15553890.1399150771546696
1.7648-1.81670.14113630.1326151411550496
1.8167-1.87530.14093640.1333151341549896
1.8753-1.94230.15843730.1431148381521194
1.9423-2.02010.12793790.1254152511563096
2.0201-2.1120.13643670.1221152661563397
2.112-2.22330.12783740.1211153271570197
2.2233-2.36250.13263670.1202149351530295
2.3625-2.54480.13373900.1182153761576698
2.5448-2.80060.13393810.1225155111589298
2.8006-3.20540.14093820.1325154691585198
3.2054-4.03630.13093720.1232151081548096
4.0363-27.4190.14463570.1287146191497692
Refinement TLS params.Method: refined / Origin x: 34.012 Å / Origin y: 10.6423 Å / Origin z: 1.12 Å
111213212223313233
T0.1045 Å2-0.0048 Å2-0.0008 Å2-0.1262 Å2-0.0035 Å2--0.1326 Å2
L0.0453 °2-0.0116 °2-0.0046 °2-0.1686 °2-0.0385 °2--0.2089 °2
S-0.0018 Å °0.0002 Å °0.0016 Å °-0.0032 Å °-0.0036 Å °-0.0126 Å °0.0012 Å °-0.0069 Å °0.0055 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 526
2X-RAY DIFFRACTION1allB3 - 526
3X-RAY DIFFRACTION1allC3 - 526
4X-RAY DIFFRACTION1allD3 - 526
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allF1 - 4
7X-RAY DIFFRACTION1allG1 - 14
8X-RAY DIFFRACTION1allS1 - 2353

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