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- PDB-1pi3: E28Q mutant Benzoylformate Decarboxylase From Pseudomonas Putida -

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Basic information

Entry
Database: PDB / ID: 1pi3
TitleE28Q mutant Benzoylformate Decarboxylase From Pseudomonas Putida
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / DECARBOXYLASE / MANDELATE CATABOLISM / THIAMIN DIPHOSPHATE / MUTANT / HIGH RESOLUTION
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
Chem-TZD / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBera, A.K. / Hasson, M.S.
Citation
Journal: To be Published
Title: High resolution structure of Benzoylformate Decarboxylate E28Q mutant
Authors: Bera, A.K. / Hasson, M.S.
#1: Journal: Biochemistry / Year: 2003
Title: STRUCTURAL AND KINETIC ANALYSIS OF CATALYSIS BY A THIAMIN DIPHOSPHATE-DEPENDENT ENZYME, BENZOYLFORMATE DECARBOXYLASE
Authors: POLOVNIKOVA, E.S. / McLeish, M.J. / Sergienko, E.A. / Burgner, J.T. / Anderson, N.L. / BERA, A.K. / Jordan, F. / Kenyon, G.L. / HASSON, M.S.
#2: 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, E.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D.
History
DepositionMay 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9876
Polymers56,4021
Non-polymers5855
Water9,080504
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)227,94624
Polymers225,6074
Non-polymers2,33920
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 area26800 Å2
ΔGint-238 kcal/mol
Surface area59020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.960, 95.528, 137.061
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-791-

HOH

31A-797-

HOH

41A-802-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFD / BFDC


Mass: 56401.762 Da / Num. of mol.: 1 / Mutation: E28Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: MDLC / Plasmid: pRep7 / Production host: Escherichia coli (E. coli) / Strain (production host): RF4738 / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O8P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.03 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 22% PEG 400, 0.15 M CaCl2, 0.5% MPD, 0.1 M TRIS-Cl (pH 8.5), 0.1 mM MgCl2, 0.2 mM TZD, 25 mM NA-HEPES (pH 7.0) VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 137252 / % possible obs: 87.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.066 / Net I/σ(I): 12.5
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.281 / % possible all: 74.2

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BFD

1bfd


Resolution: 1.2→20 Å / Num. parameters: 40857 / Num. restraintsaints: 49155 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.136 7287 0.05 %RANDOM
obs0.121 -87.6 %-
all-165003 --
Displacement parametersBiso mean: 14.77 Å2
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 3825.35 / Occupancy sum non hydrogen: 4406.93
FreeObs
Luzzati coordinate error0.11 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 31 504 4463
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.062
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.079
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.2-1.250.202X-RAY DIFFRACTION575.7
1.25-1.40.152X-RAY DIFFRACTION588.61
1.4-1.50.121X-RAY DIFFRACTION590.33
1.5-20.099X-RAY DIFFRACTION588.72
2-50.116X-RAY DIFFRACTION572.52

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