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- PDB-4gm4: Crystal Structure of Benzoylformate Decarboxylase Mutant L403I -

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Basic information

Entry
Database: PDB / ID: 4gm4
TitleCrystal Structure of Benzoylformate Decarboxylase Mutant L403I
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: 1.28 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.name
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
Polymers57,4761
Non-polymers7286
Water9,080504
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)232,81428
Polymers229,9044
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 area29140 Å2
ΔGint-219 kcal/mol
Surface area58700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.146, 95.768, 137.002
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-606-

NA

21A-702-

HOH

31A-720-

HOH

41A-837-

HOH

51A-1037-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Benzoylformate decarboxylase / BFD / BFDC


Mass: 57475.914 Da / Num. of mol.: 1 / Mutation: L403I
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, 510 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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: 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.: 504 / 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: 46.88 %
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: 14-ID-B / Wavelength: 0.69 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.69 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 136365 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.066 / Χ2: 1.009 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.28-1.336.60.712134600.924199
1.33-1.3870.58134800.909199.2
1.38-1.447.30.453134850.891199.3
1.44-1.527.50.325135190.898199.4
1.52-1.617.60.225135590.942199.6
1.61-1.747.60.158136130.937199.7
1.74-1.917.60.095136850.94199.8
1.91-2.197.60.063136851.141199.9
2.19-2.767.60.043137971.2041100
2.76-507.40.031140821.266199.4

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Processing

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

1bfd


Resolution: 1.28→36.043 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.11 / σ(F): 1.34 / Phase error: 14.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1587 6839 5.02 %
Rwork0.1376 --
obs0.1386 136308 99.23 %
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.944 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 81.9 Å2 / Biso mean: 15.2364 Å2 / Biso min: 2.69 Å2
Baniso -1Baniso -2Baniso -3
1-2.7364 Å2-0 Å2-0 Å2
2---0.9781 Å20 Å2
3----1.7583 Å2
Refinement stepCycle: LAST / Resolution: 1.28→36.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 42 504 4487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164232
X-RAY DIFFRACTIONf_angle_d1.735813
X-RAY DIFFRACTIONf_chiral_restr0.105643
X-RAY DIFFRACTIONf_plane_restr0.011775
X-RAY DIFFRACTIONf_dihedral_angle_d13.4451559
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 (%)
1.28-1.29280.23842170.20443974419191
1.2928-1.3080.25852130.19794288450199
1.308-1.32390.23142110.18344256446799
1.3239-1.34070.21212590.17384190444999
1.3407-1.35830.20522340.164282451699
1.3583-1.37690.18522370.15524290452799
1.3769-1.39660.21992390.15614248448799
1.3966-1.41740.17952220.15484276449899
1.4174-1.43960.18072370.14284271450899
1.4396-1.46320.16471930.13824325451899
1.4632-1.48840.16772180.13424291450999
1.4884-1.51550.15932350.12974302453799
1.5155-1.54460.16162260.12664310453699
1.5446-1.57620.14072340.127543154549100
1.5762-1.61040.162470.121842654512100
1.6104-1.64790.14972080.119643274535100
1.6479-1.68910.16222180.120543564574100
1.6891-1.73480.1632290.124242924521100
1.7348-1.78580.16672410.121243324573100
1.7858-1.84350.14512230.115543474570100
1.8435-1.90940.16222370.119143194556100
1.9094-1.98580.15222100.125943674577100
1.9858-2.07620.1442100.124143674577100
2.0762-2.18560.14222430.125443294572100
2.1856-2.32250.14392270.124344014628100
2.3225-2.50180.1422260.129243784604100
2.5018-2.75350.15282460.134343604606100
2.7535-3.15170.14472210.138944334654100
3.1517-3.97010.13182340.136944494683100
3.9701-36.0430.17812440.16324529477398

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