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- PDB-4jua: Crystal Structure of the His70Ser mutant of Benzoylformate Decarb... -

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Basic information

Entry
Database: PDB / ID: 4jua
TitleCrystal Structure of the His70Ser 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
Chem-TZD / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMcLeish, M.J. / Brodkin, H.R.
CitationJournal: To be Published
Title: Crystal Structure of the His70Ser 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
DepositionMar 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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

Downloads & links

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7346
Polymers57,1811
Non-polymers5535
Water10,899605
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)230,93524
Polymers228,7224
Non-polymers2,21320
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 area27380 Å2
ΔGint-254 kcal/mol
Surface area59980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.348, 95.161, 137.065
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-604-

MG

21A-717-

HOH

31A-784-

HOH

41A-921-

HOH

51A-1116-

HOH

61A-1156-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFD / BFDC


Mass: 57180.570 Da / Num. of mol.: 1 / Mutation: H70S
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#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.: 605 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
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: Aug 4, 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: 1.15→41.487 Å / Num. all: 157119 / Num. obs: 157037 / % possible obs: 83.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.4
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.8 / % possible all: 25.3

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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: 1.15→41.187 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 14.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1503 1999 1.27 %
Rwork0.1317 --
obs0.1319 157037 83.86 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 116.124 Å2 / ksol: 0.515 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2069 Å2-0 Å20 Å2
2---2.396 Å20 Å2
3---1.1891 Å2
Refinement stepCycle: LAST / Resolution: 1.15→41.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 31 605 4573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054183
X-RAY DIFFRACTIONf_angle_d1.1585749
X-RAY DIFFRACTIONf_dihedral_angle_d12.3891549
X-RAY DIFFRACTIONf_chiral_restr0.077645
X-RAY DIFFRACTIONf_plane_restr0.007761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.17910.2954370.29312884X-RAY DIFFRACTION22
1.1791-1.21090.2724640.22814911X-RAY DIFFRACTION37
1.2109-1.24660.2301920.19457158X-RAY DIFFRACTION55
1.2466-1.28680.22121240.17319585X-RAY DIFFRACTION73
1.2868-1.33280.17511510.141311789X-RAY DIFFRACTION90
1.3328-1.38620.13251690.121412992X-RAY DIFFRACTION99
1.3862-1.44930.13331690.112213111X-RAY DIFFRACTION100
1.4493-1.52570.1191690.10713131X-RAY DIFFRACTION100
1.5257-1.62130.12861680.106913144X-RAY DIFFRACTION100
1.6213-1.74650.13591710.111713213X-RAY DIFFRACTION100
1.7465-1.92220.14821700.123213216X-RAY DIFFRACTION100
1.9222-2.20030.14411710.122913270X-RAY DIFFRACTION100
2.2003-2.77210.13261720.128413322X-RAY DIFFRACTION100
2.7721-41.21360.16661720.145813312X-RAY DIFFRACTION97

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