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- PDB-4gp9: Crystal Structure of Benzoylformate Decarboxylase Mutant L403F -

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Basic information

Entry
Database: PDB / ID: 4gp9
TitleCrystal Structure of Benzoylformate Decarboxylase Mutant L403F
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 20, 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)58,2387
Polymers57,5101
Non-polymers7286
Water10,971609
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)232,95028
Polymers230,0404
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 area29160 Å2
ΔGint-214 kcal/mol
Surface area59100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.245, 95.550, 137.355
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-711-

HOH

31A-716-

HOH

41A-844-

HOH

51A-1188-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Benzoylformate decarboxylase / / BFD / BFDC


Mass: 57509.930 Da / Num. of mol.: 1 / Mutation: L403F
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, 615 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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 / Water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 46.93 %
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
RadiationProtocol: 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: 217292 / % possible obs: 93.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.063 / Χ2: 0.999 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.07-1.112.90.572133170.955157.6
1.11-1.153.70.427184230.971179.8
1.15-1.215.50.344219251.006194.6
1.21-1.276.80.284231721.0511100
1.27-1.356.90.209232291.0441100
1.35-1.457.10.158232581.151100
1.45-1.67.20.111232151.0421100
1.6-1.837.60.075233660.9931100
1.83-2.3110.80.069234410.9671100
2.31-5014.50.049239460.9041100

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Processing

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

1bfd


Resolution: 1.07→45.978 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.08 / σ(F): 1.34 / Phase error: 13.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1503 10840 4.99 %RANDOM
Rwork0.1373 ---
obs0.1379 217223 93.16 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.298 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 68.97 Å2 / Biso mean: 12.628 Å2 / Biso min: 2.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.6708 Å20 Å2-0 Å2
2---1.4524 Å20 Å2
3----1.2184 Å2
Refinement stepCycle: LAST / Resolution: 1.07→45.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 42 609 4595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134305
X-RAY DIFFRACTIONf_angle_d1.6025924
X-RAY DIFFRACTIONf_chiral_restr0.095653
X-RAY DIFFRACTIONf_plane_restr0.01791
X-RAY DIFFRACTIONf_dihedral_angle_d13.4891602
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 (%)
1.07-1.08250.32391880.29963534372248
1.0825-1.09520.26242200.26484201442157
1.0952-1.10860.24482560.23274805506166
1.1086-1.12260.24852830.21445397568073
1.1226-1.13740.21333020.19845877617980
1.1374-1.15290.22063190.17816225654485
1.1529-1.16940.1833320.16036613694590
1.1694-1.18690.17423730.1476916728994
1.1869-1.20540.17053470.1387355770299
1.2054-1.22520.17533480.130873687716100
1.2252-1.24630.14843960.129473147710100
1.2463-1.2690.14753850.126673727757100
1.269-1.29340.14713650.123673757740100
1.2934-1.31980.14133890.119873247713100
1.3198-1.34850.14013790.12573907769100
1.3485-1.37990.14913580.1273747732100
1.3799-1.41440.14483820.118773297711100
1.4144-1.45260.13863840.1274457829100
1.4526-1.49540.14423830.118173457728100
1.4954-1.54360.12663990.115473377736100
1.5436-1.59880.13713940.113473737767100
1.5988-1.66280.13344020.114774027804100
1.6628-1.73850.13993930.119873527745100
1.7385-1.83020.14053840.120774327816100
1.8302-1.94480.12654000.13174177817100
1.9448-2.0950.13674070.130373817788100
2.095-2.30580.1454010.133674427843100
2.3058-2.63940.14224240.137174457869100
2.6394-3.32530.15544040.146575387942100
3.3253-45.9780.15254430.150577058148100

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