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- PDB-4k9m: Crystal Structure of the His281Asn mutant of Benzoylformate Decar... -

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Basic information

Entry
Database: PDB / ID: 4k9m
TitleCrystal Structure of the His281Asn 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: 1.15 Å
AuthorsBrodkin, H.R. / McLeish, M.J.
CitationJournal: To be Published
Title: Crystal Structure of the His281Asn 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
DepositionApr 20, 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_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

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Assembly

Deposited unit
A: Benzoylformate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2896
Polymers56,7511
Non-polymers5385
Water11,295627
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)229,15724
Polymers227,0044
Non-polymers2,15320
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 area27570 Å2
ΔGint-315 kcal/mol
Surface area59870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.192, 95.596, 137.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-604-

MG

21A-710-

HOH

31A-718-

HOH

41A-887-

HOH

51A-895-

HOH

61A-1112-

HOH

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Components

#1: Protein Benzoylformate decarboxylase / / BFD / BFDC


Mass: 56750.969 Da / Num. of mol.: 1 / Mutation: H281N
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
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
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: Mar 3, 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: 1.15→23 Å / Num. all: 150739 / Num. obs: 150662 / % possible obs: 80.4 % / Redundancy: 12.9 %
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.7 / % possible all: 16.9

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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: 1.15→22.963 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 15.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1509 2000 1.33 %
Rwork0.1414 --
obs0.1415 150662 80.29 %
all-150739 -
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 111.301 Å2 / ksol: 0.48 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9942 Å20 Å20 Å2
2--1.9035 Å2-0 Å2
3---2.0907 Å2
Refinement stepCycle: LAST / Resolution: 1.15→22.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 30 627 4583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074129
X-RAY DIFFRACTIONf_angle_d1.1285669
X-RAY DIFFRACTIONf_dihedral_angle_d12.9351513
X-RAY DIFFRACTIONf_chiral_restr0.091642
X-RAY DIFFRACTIONf_plane_restr0.008749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1504-1.17920.3424240.28181786X-RAY DIFFRACTION14
1.1792-1.21110.3292520.25583835X-RAY DIFFRACTION29
1.2111-1.24670.2169830.22546187X-RAY DIFFRACTION47
1.2467-1.2870.22811100.19978132X-RAY DIFFRACTION62
1.287-1.33290.1761410.176610510X-RAY DIFFRACTION80
1.3329-1.38630.1841710.15712669X-RAY DIFFRACTION96
1.3863-1.44940.17231740.141712940X-RAY DIFFRACTION98
1.4494-1.52580.13931740.127912966X-RAY DIFFRACTION99
1.5258-1.62140.13721750.12613054X-RAY DIFFRACTION99
1.6214-1.74650.14091770.128913123X-RAY DIFFRACTION99
1.7465-1.92220.16191780.132613213X-RAY DIFFRACTION100
1.9222-2.20010.15061780.131413267X-RAY DIFFRACTION100
2.2001-2.77120.1471790.135613351X-RAY DIFFRACTION100
2.7712-22.96730.131840.141113629X-RAY DIFFRACTION99

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