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- PDB-4gm0: Crystal Structure of Benzoylformate Decarboxylase Mutant L403N -

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Basic information

Entry
Database: PDB / ID: 4gm0
TitleCrystal Structure of Benzoylformate Decarboxylase Mutant L403N
ComponentsBenzoylformate decarboxylase
KeywordsLYASE / DECARBOXYLASE / THIAMIN THIAZOLONE DIPHOSPHATE COFACTOR
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: 1.07 Å
AuthorsNovak, W.R.P. / Andrews, F.H. / Tom, A.R. / Gunderman, P.R. / McLeish, M.J.
CitationJournal: Biochemistry / Year: 2013
Title: A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate.
Authors: Andrews, F.H. / Tom, A.R. / Gunderman, P.R. / Novak, W.R. / McLeish, M.J.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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)58,2047
Polymers57,4771
Non-polymers7286
Water10,395577
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)232,81828
Polymers229,9074
Non-polymers2,91124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area29440 Å2
ΔGint-207 kcal/mol
Surface area57990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.445, 95.685, 136.881
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-605-

NA

21A-716-

HOH

31A-739-

HOH

41A-857-

HOH

51A-996-

HOH

61A-1080-

HOH

71A-1154-

HOH

81A-1194-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Benzoylformate decarboxylase / BFD / BFDC


Mass: 57476.859 Da / Num. of mol.: 1 / Mutation: L403N
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

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Non-polymers , 5 types, 583 molecules

#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 46.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 22% v/v PEG 400, 150 mM CaCl2, 0.5% v/v MPD [2-METHYL-2,4-PENTANEDIOL], 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 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.07→50 Å / Num. obs: 216844 / Observed criterion σ(I): 1.48

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BFD

1bfd


Resolution: 1.07→45.957 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.08 / σ(F): 1.34 / Phase error: 13.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1509 10897 5.03 %RANDOM
Rwork0.1373 ---
obs0.138 216785 92.97 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.802 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 55.97 Å2 / Biso mean: 11.9197 Å2 / Biso min: 4.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.1681 Å2-0 Å2-0 Å2
2---1.4268 Å2-0 Å2
3----0.7414 Å2
Refinement stepCycle: LAST / Resolution: 1.07→45.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 42 577 4560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154305
X-RAY DIFFRACTIONf_angle_d1.6475918
X-RAY DIFFRACTIONf_chiral_restr0.098647
X-RAY DIFFRACTIONf_plane_restr0.011798
X-RAY DIFFRACTIONf_dihedral_angle_d13.0451579
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 (%)
1.07-1.08270.34261980.31843626382450
1.0827-1.09540.2991860.27454331451758
1.0954-1.10880.23672300.23294774500465
1.1088-1.12280.22212580.20485249550771
1.1228-1.13760.19952910.18895710600178
1.1376-1.15320.20343240.17016243656785
1.1532-1.16960.16633270.1566770709792
1.1696-1.18710.15963780.14147114749297
1.1871-1.20560.14574070.1337227763499
1.2056-1.22540.14853870.12617248763599
1.2254-1.24650.14563690.1257268763799
1.2465-1.26920.13573800.12287298767899
1.2692-1.29360.14683790.12347311769099
1.2936-1.320.14143570.12037300765799
1.32-1.34870.15313720.12087331770399
1.3487-1.38010.13734260.118472877713100
1.3801-1.41460.13473770.124673357712100
1.4146-1.45290.13563770.119373757752100
1.4529-1.49560.14964030.116673317734100
1.4956-1.54390.12614310.112673027733100
1.5439-1.59910.12254000.112673657765100
1.5991-1.66310.13953700.113773937763100
1.6631-1.73880.12974250.118673497774100
1.7388-1.83050.143970.120973817778100
1.8305-1.94520.14044080.130374177825100
1.9452-2.09540.13333800.132374327812100
2.0954-2.30620.14754000.134374327832100
2.3062-2.63990.14934080.139674667874100
2.6399-3.32590.16274190.147475157934100
3.3259-45.9570.16064330.15377088141100

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