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- PDB-4k9k: Crystal Structure of the His281Tyr mutant of Benzoylformate Decar... -

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Basic information

Entry
Database: PDB / ID: 4k9k
TitleCrystal Structure of the His281Tyr 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: 1.301 Å
AuthorsBrodkin, H.R. / McLeish, M.J.
CitationJournal: To be Published
Title: Crystal Structure of the His281Tyr 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_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_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.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_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

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3386
Polymers56,8001
Non-polymers5385
Water11,205622
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)229,35324
Polymers227,2004
Non-polymers2,15320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area27370 Å2
ΔGint-276 kcal/mol
Surface area58720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.263, 95.484, 136.814
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-603-

MG

21A-721-

HOH

31A-741-

HOH

41A-907-

HOH

51A-1296-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFD / BFDC


Mass: 56800.039 Da / Num. of mol.: 1 / Mutation: H281Y
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
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
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: 1.3→22.946 Å / Num. all: 125760 / Num. obs: 125725 / % possible obs: 96.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 3.3 / % possible all: 78.4

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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: 1.301→22.946 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 15.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1538 1999 1.59 %
Rwork0.1394 --
obs0.1396 125725 96.78 %
all-125760 -
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.918 Å2 / ksol: 0.451 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9169 Å2-0 Å20 Å2
2---2.2331 Å2-0 Å2
3---3.1501 Å2
Refinement stepCycle: LAST / Resolution: 1.301→22.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 30 622 4588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074116
X-RAY DIFFRACTIONf_angle_d1.0435647
X-RAY DIFFRACTIONf_dihedral_angle_d13.5211501
X-RAY DIFFRACTIONf_chiral_restr0.066635
X-RAY DIFFRACTIONf_plane_restr0.009748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.301-1.33350.25591050.23996496X-RAY DIFFRACTION72
1.3335-1.36950.26051360.21268412X-RAY DIFFRACTION93
1.3695-1.40980.20421440.1838887X-RAY DIFFRACTION98
1.4098-1.45530.18871440.15138911X-RAY DIFFRACTION98
1.4553-1.50730.15221440.13558931X-RAY DIFFRACTION98
1.5073-1.56770.15811450.12768960X-RAY DIFFRACTION99
1.5677-1.6390.17081460.12588986X-RAY DIFFRACTION99
1.639-1.72540.16371450.12959031X-RAY DIFFRACTION99
1.7254-1.83350.16141450.12789030X-RAY DIFFRACTION99
1.8335-1.97490.16641480.13489112X-RAY DIFFRACTION100
1.9749-2.17360.15381470.13469127X-RAY DIFFRACTION100
2.1736-2.48780.1441480.12999175X-RAY DIFFRACTION100
2.4878-3.1330.14571490.13869250X-RAY DIFFRACTION100
3.133-22.94970.12971530.13889418X-RAY DIFFRACTION99

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