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- PDB-4mq5: Crystal Structure of Benzoylformate Decarboxylase Mutant A306F -

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Basic information

Entry
Database: PDB / ID: 4mq5
TitleCrystal Structure of Benzoylformate Decarboxylase Mutant A306F
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / ThDP-dependent / cytol
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: 1.502 Å
AuthorsAndrews, F.H. / McLeish, M.J.
CitationJournal: Biochemistry / Year: 2014
Title: Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer.
Authors: Andrews, F.H. / Rogers, M.P. / Paul, L.N. / McLeish, M.J.
History
DepositionSep 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)58,1447
Polymers57,5521
Non-polymers5926
Water10,557586
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)232,57428
Polymers230,2084
Non-polymers2,36624
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 area27880 Å2
ΔGint-305 kcal/mol
Surface area59660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.629, 95.540, 137.590
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-606-

CA

21A-734-

HOH

31A-754-

HOH

41A-866-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFD / BFDC


Mass: 57552.008 Da / Num. of mol.: 1 / Mutation: A306F
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) / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium, 22% v/v PEG400, 0.15 M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 85510 / Num. obs: 85254 / % possible obs: 99.7 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.5→1.53 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.502→26.443 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 12.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1472 2000 2.35 %RANDOM
Rwork0.1196 ---
obs0.1203 85253 99.43 %-
all-85510 --
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.502→26.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 31 586 4557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094254
X-RAY DIFFRACTIONf_angle_d1.2895842
X-RAY DIFFRACTIONf_dihedral_angle_d13.0621564
X-RAY DIFFRACTIONf_chiral_restr0.086647
X-RAY DIFFRACTIONf_plane_restr0.008779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.502-1.53930.14581370.09595678X-RAY DIFFRACTION96
1.5393-1.58090.141420.09255924X-RAY DIFFRACTION100
1.5809-1.62740.1581420.09025911X-RAY DIFFRACTION100
1.6274-1.680.13221410.09145912X-RAY DIFFRACTION100
1.68-1.740.1621430.09955936X-RAY DIFFRACTION100
1.74-1.80970.17311430.10365949X-RAY DIFFRACTION100
1.8097-1.8920.15211430.10675942X-RAY DIFFRACTION100
1.892-1.99170.11781440.10655980X-RAY DIFFRACTION100
1.9917-2.11640.14411420.11075964X-RAY DIFFRACTION100
2.1164-2.27980.14091440.1175973X-RAY DIFFRACTION100
2.2798-2.5090.14391440.12315988X-RAY DIFFRACTION100
2.509-2.87170.16291450.13475995X-RAY DIFFRACTION100
2.8717-3.61660.16471450.1356076X-RAY DIFFRACTION100
3.6166-26.44710.13321450.13316025X-RAY DIFFRACTION96

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