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- PDB-5dgt: BENZOYLFORMATE DECARBOXYLASE H70A MUTANT at pH 8.5 FROM PSEUDOMON... -

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Basic information

Entry
Database: PDB / ID: 5dgt
TitleBENZOYLFORMATE DECARBOXYLASE H70A MUTANT at pH 8.5 FROM PSEUDOMONAS PUTIDA
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / BENZOYLFORMATE DECARBOXYLASE THIAMIN THIAZOLONE 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: 1.081 Å
AuthorsBera, A.K. / Hasson, M.S.
Citation
Journal: to be published
Title: BENZOYLFORMATE DECARBOXYLASE H70A MUTANT at pH 8.5 FROM PSEUDOMONAS PUTIDA
Authors: Bera, A.K. / Hasson, M.S.
#1: Journal: J.Am.Chem.Soc. / Year: 2007
Title: Mechanism-based inactivation of benzoylformate decarboxylase, a thiamin diphosphate-dependent enzyme.
Authors: Bera, A.K. / Polovnikova, L.S. / Roestamadji, J. / Widlanski, T.S. / Kenyon, G.L. / McLeish, M.J. / Hasson, M.S.
History
DepositionAug 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_symmetry

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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)56,4646
Polymers55,8791
Non-polymers5855
Water13,205733
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)225,85624
Polymers223,5164
Non-polymers2,33920
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 area26970 Å2
ΔGint-233 kcal/mol
Surface area59560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.341, 94.802, 137.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-601-

MG

21A-966-

HOH

31A-1024-

HOH

41A-1030-

HOH

51A-1207-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / BFDC


Mass: 55879.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC / Plasmid: PREP7 / Production host: Escherichia coli (E. coli) / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% (V/V) PEG400, 0.15 M CACl2, 0.5% (V/V), MPD, 0.1 M TRISCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 213422 / % possible obs: 94.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.66 Å2 / Rsym value: 0.094 / Net I/σ(I): 12.2
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.28 / % possible all: 92.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFD

1bfd


Resolution: 1.081→19.505 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1501 10706 5.02 %
Rwork0.1431 202644 -
obs0.1435 213350 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.19 Å2 / Biso mean: 16.0035 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 1.081→19.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 46 733 4708
Biso mean--11.48 27.42 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124140
X-RAY DIFFRACTIONf_angle_d1.4965688
X-RAY DIFFRACTIONf_chiral_restr0.09637
X-RAY DIFFRACTIONf_plane_restr0.01757
X-RAY DIFFRACTIONf_dihedral_angle_d12.4771513
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0808-1.09310.23893070.23246220652788
1.0931-1.10590.21583130.21626544685792
1.1059-1.11940.20483980.19556683708195
1.1194-1.13360.19893790.1926808718797
1.1336-1.14850.17913580.18236866722497
1.1485-1.16420.18653520.17776832718496
1.1642-1.18090.17323510.16936847719897
1.1809-1.19850.17893630.16946864722798
1.1985-1.21720.16713670.16296937730498
1.2172-1.23720.16763780.15916939731798
1.2372-1.25850.14973590.15486875723498
1.2585-1.28140.17013560.156942729898
1.2814-1.3060.15473840.14266985736998
1.306-1.33270.15384010.14236958735999
1.3327-1.36160.15823790.13976936731598
1.3616-1.39330.1493130.13437038735198
1.3933-1.42810.13893710.13187043741499
1.4281-1.46670.12683530.12887052740599
1.4667-1.50990.15343650.12667071743699
1.5099-1.55860.13263620.12337075743799
1.5586-1.61430.14063840.11967022740699
1.6143-1.67890.12633990.12227041744099
1.6789-1.75520.13794140.12127064747899
1.7552-1.84770.12973710.12047017738898
1.8477-1.96340.14133780.1236918729697
1.9634-2.11480.1273390.12346852719195
2.1148-2.32730.12453390.12476583692291
2.3273-2.66340.14493530.1326344669788
2.6634-3.35280.15152980.15176026632483
3.3528-19.50820.19862220.21184262448457

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