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- PDB-4k9o: Crystal Structure of the Phe397Ala mutant of Benzoylformate Decar... -

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Basic information

Entry
Database: PDB / ID: 4k9o
TitleCrystal Structure of the Phe397Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / Thiamine Diphosphate
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
THIAMINE DIPHOSPHATE / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.888 Å
AuthorsBrodkin, H.R. / McLeish, M.J.
CitationJournal: To be Published
Title: Crystal Structure of the Phe397Ala mutant of Benzoylformate Decarboxylase from Pseudomonas putida
Authors: Brodkin, H.R. / Andrews, F.H. / Milne, A.C. / Petsko, G.A. / Ringe, D. / McLeish, M.J.
History
DepositionApr 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_asym_id / _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.ptnr2_auth_asym_id / _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_asym_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.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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
B: Benzoylformate decarboxylase
C: Benzoylformate decarboxylase
D: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,56020
Polymers228,0974
Non-polymers2,46316
Water23,5821309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27960 Å2
ΔGint-217 kcal/mol
Surface area60020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.183, 161.218, 175.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Benzoylformate decarboxylase / BFD / BFDC


Mass: 57024.344 Da / Num. of mol.: 4 / Mutation: F397A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P20906, benzoylformate decarboxylase

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Non-polymers , 5 types, 1325 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1309 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.888→38.5 Å / Num. all: 158398 / Num. obs: 149426 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.7
Reflection shellResolution: 1.888→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BlueIce-Epicsdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BFD

1bfd


Resolution: 1.888→38.486 Å / SU ML: 0.33 / σ(F): 0.09 / Phase error: 19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1917 1991 1.33 %
Rwork0.1671 --
obs0.1674 149426 93.48 %
all-158398 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.332 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8186 Å20 Å20 Å2
2--1.303 Å2-0 Å2
3---1.5155 Å2
Refinement stepCycle: LAST / Resolution: 1.888→38.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15726 0 146 1309 17181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116376
X-RAY DIFFRACTIONf_angle_d1.23922425
X-RAY DIFFRACTIONf_dihedral_angle_d14.3295933
X-RAY DIFFRACTIONf_chiral_restr0.0662506
X-RAY DIFFRACTIONf_plane_restr0.012971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8881-1.93530.29671100.2568047X-RAY DIFFRACTION72
1.9353-1.98770.25381300.22529522X-RAY DIFFRACTION86
1.9877-2.04610.27991240.21399890X-RAY DIFFRACTION89
2.0461-2.11220.24621380.199610168X-RAY DIFFRACTION91
2.1122-2.18770.21691450.192910385X-RAY DIFFRACTION93
2.1877-2.27530.22211400.181210535X-RAY DIFFRACTION94
2.2753-2.37880.22271310.172910644X-RAY DIFFRACTION95
2.3788-2.50420.21441540.180510828X-RAY DIFFRACTION96
2.5042-2.6610.24171520.174110922X-RAY DIFFRACTION97
2.661-2.86640.20691460.174811062X-RAY DIFFRACTION98
2.8664-3.15480.1931440.174911137X-RAY DIFFRACTION99
3.1548-3.6110.17641600.159511231X-RAY DIFFRACTION99
3.611-4.54830.15281530.134611322X-RAY DIFFRACTION99
4.5483-38.49430.15621640.153211742X-RAY DIFFRACTION99

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