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- PDB-4jub: Crystal Structure of the His70Thr mutant of Benzoylformate Decarb... -

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Basic information

Entry
Database: PDB / ID: 4jub
TitleCrystal Structure of the His70Thr 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: 1.901 Å
AuthorsMcLeish, M.J. / Brodkin, H.R.
CitationJournal: To be Published
Title: Crystal Structure of the His70Thr 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 1.0May 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)230,80516
Polymers228,7784
Non-polymers2,02712
Water23,6721314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27120 Å2
ΔGint-218 kcal/mol
Surface area59420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.465, 161.682, 175.874
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: 57194.594 Da / Num. of mol.: 4 / Mutation: H70T
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, 1326 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1314 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
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: 1.901→47.459 Å / Num. all: 152025 / Num. obs: 151573 / % possible obs: 96.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 1.901→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.4 / % possible all: 72.7

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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: 1.901→47.459 Å / SU ML: 0.42 / σ(F): 1.33 / Phase error: 19.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.203 7612 5.02 %
Rwork0.1661 --
obs0.168 151573 95.82 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.629 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0969 Å20 Å2-0 Å2
2--2.3379 Å20 Å2
3----3.4348 Å2
Refinement stepCycle: LAST / Resolution: 1.901→47.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15724 0 117 1314 17155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716281
X-RAY DIFFRACTIONf_angle_d1.09222280
X-RAY DIFFRACTIONf_dihedral_angle_d12.9275873
X-RAY DIFFRACTIONf_chiral_restr0.0742507
X-RAY DIFFRACTIONf_plane_restr0.0052947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9015-1.92310.33291840.30223116X-RAY DIFFRACTION64
1.9231-1.94570.32121840.28953612X-RAY DIFFRACTION73
1.9457-1.96940.31662110.28323933X-RAY DIFFRACTION79
1.9694-1.99440.32432070.2764218X-RAY DIFFRACTION85
1.9944-2.02060.31932350.24714488X-RAY DIFFRACTION90
2.0206-2.04830.2872330.23764608X-RAY DIFFRACTION93
2.0483-2.07750.29472550.22464817X-RAY DIFFRACTION97
2.0775-2.10860.25652680.20694813X-RAY DIFFRACTION98
2.1086-2.14150.26872750.19354941X-RAY DIFFRACTION99
2.1415-2.17660.22242620.18424929X-RAY DIFFRACTION99
2.1766-2.21410.24182590.17894965X-RAY DIFFRACTION99
2.2141-2.25440.23392750.17464937X-RAY DIFFRACTION99
2.2544-2.29780.22962410.16764925X-RAY DIFFRACTION100
2.2978-2.34470.21812600.15565019X-RAY DIFFRACTION100
2.3447-2.39570.19442430.15814932X-RAY DIFFRACTION100
2.3957-2.45140.21742320.16945027X-RAY DIFFRACTION100
2.4514-2.51270.22262870.16894956X-RAY DIFFRACTION100
2.5127-2.58060.22452600.16384948X-RAY DIFFRACTION100
2.5806-2.65650.20432480.16245025X-RAY DIFFRACTION100
2.6565-2.74230.22582780.16074984X-RAY DIFFRACTION100
2.7423-2.84030.19592730.16085004X-RAY DIFFRACTION100
2.8403-2.9540.20182900.16254991X-RAY DIFFRACTION100
2.954-3.08840.21462630.16855000X-RAY DIFFRACTION100
3.0884-3.25120.18442800.16315010X-RAY DIFFRACTION100
3.2512-3.45480.18292740.15575039X-RAY DIFFRACTION100
3.4548-3.72150.15392670.14895061X-RAY DIFFRACTION100
3.7215-4.09580.16032630.13085064X-RAY DIFFRACTION100
4.0958-4.6880.14292620.11925103X-RAY DIFFRACTION100
4.688-5.90460.16522550.13525164X-RAY DIFFRACTION100
5.9046-47.47370.18592880.17615332X-RAY DIFFRACTION100

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