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- PDB-2uz1: 1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-me... -

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Basic information

Entry
Database: PDB / ID: 2uz1
Title1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-methyl- 2,4-pentanediol
Components(BENZALDEHYDE LYASE) x 2
KeywordsLYASE / THIAMINE DIPHOSPHATE / THIAMINE PYROPHOSPHATE / BENZOIN / FLAVOPROTEIN / BENZALDEHYDE
Function / homology
Function and homology information


acetolactate synthase complex / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / lyase activity / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / 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 ...Thiamine pyrophosphate enzyme / 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 / Benzaldehyde lyase
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMaraite, A. / Schmidt, T. / Ansorge-Schumacher, M.B. / Brzozowski, A.M. / Grogan, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Structure of the Thdp-Dependent Enzyme Benzaldehyde Lyase Refined to 1.65 A Resolution.
Authors: Maraite, A. / Schmidt, T. / Ansorge-Schumacher, M.B. / Brzozowski, A.M. / Grogan, G.
History
DepositionApr 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BENZALDEHYDE LYASE
B: BENZALDEHYDE LYASE
C: BENZALDEHYDE LYASE
D: BENZALDEHYDE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,96011
Polymers235,9044
Non-polymers2,0567
Water33,8861881
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.462, 121.601, 162.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BENZALDEHYDE LYASE


Mass: 58976.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: BIOVAR I / Description: RECOMBINANT FROM EXPRESSION PLASMID IN E. COLI / Plasmid: PBALHIS6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F4L3, EC: 4.1.2.38
#2: Protein BENZALDEHYDE LYASE


Mass: 58976.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: BIOVAR I / Description: RECOMBINANT FROM EXPRESSION PLASMID IN E. COLI / Plasmid: PBALHIS6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F4L3, EC: 4.1.2.38
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1881 / 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: 1 Å3/Da / Density % sol: 37 %
Crystal growpH: 7.5
Details: 0.1 M TRIS/HCL, PH 7.5, 0.2 M POTASSIUM ISOTHIOCYANATE, 10% (W/V) POLYETHYLENE GLYCOL 1000 MW, 10% POLYETHYLENE GLYCOL 8000 MW, AND 2-METHYLPENTANE-2-4-DIOL 45% (V/V); PROTEIN CONCENTRATION ...Details: 0.1 M TRIS/HCL, PH 7.5, 0.2 M POTASSIUM ISOTHIOCYANATE, 10% (W/V) POLYETHYLENE GLYCOL 1000 MW, 10% POLYETHYLENE GLYCOL 8000 MW, AND 2-METHYLPENTANE-2-4-DIOL 45% (V/V); PROTEIN CONCENTRATION 5 MG ML-1 WITH A THREEFOLD STOICHIOMETRIC EXCESS OF THIAMINE DIPHOSPHATE (THDP).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 249612 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AG0

2ag0


Resolution: 1.65→97.59 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.739 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 12534 5 %RANDOM
Rwork0.167 ---
obs0.168 236875 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.75 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.65→97.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16184 0 126 1881 18191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02116778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.96322950
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60852264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23823.532637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38152458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.715104
X-RAY DIFFRACTIONr_chiral_restr0.0830.22690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.28959
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.211699
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.21734
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5611.511036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.967217581
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.83535930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8774.55344
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 940
Rwork0.25 16809

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