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- PDB-2ag1: Crystal structure of Benzaldehyde lyase (BAL)- SeMet -

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Basic information

Entry
Database: PDB / ID: 2ag1
TitleCrystal structure of Benzaldehyde lyase (BAL)- SeMet
Componentsbenzaldehyde lyase
KeywordsLYASE / ThDP dependent fold / tetramer
Function / homology
Function and homology information


thiamine pyrophosphate binding / carboxylic acid metabolic process / 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 / MAD / Resolution: 2.58 Å
AuthorsMosbacher, T.G. / Mueller, M. / Schulz, G.E.
CitationJournal: Febs J. / Year: 2005
Title: Structure and mechanism of the ThDP-dependent benzaldehyde lyase from Pseudomonas fluorescens
Authors: Mosbacher, T.G. / Mueller, M. / Schulz, G.E.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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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)240,14112
Polymers238,3434
Non-polymers1,7988
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24100 Å2
ΔGint-154 kcal/mol
Surface area62660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.165, 150.165, 195.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 3 - 555 / Label seq-ID: 3 - 555

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
Detailsthe biological assembly is a tetramer which is respresented by the contains of the assymtetric unit (Chains A, B, C, D)

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Components

#1: Protein
benzaldehyde lyase


Mass: 59585.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: puc18 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 prep4
References: GenBank: 9965498, UniProt: Q9F4L3*PLUS, EC: 4.1.2.38
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 200, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9793, 0.9801, 0.9393
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 14, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.98011
30.93931
ReflectionResolution: 2.5→35 Å / Num. all: 157089 / Num. obs: 156247 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.095 / Rsym value: 0.082 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.7 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.58→24.82 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.896 / SU B: 23.323 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R: 0.749 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24496 4037 5 %RANDOM
Rwork0.2116 ---
all0.214 82005 --
obs0.21328 76469 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.673 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20.77 Å20 Å2
2--1.53 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.58→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16296 0 112 400 16808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216736
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.96122840
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23852208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31823.795664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01152504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.32615104
X-RAY DIFFRACTIONr_chiral_restr0.1020.22652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.28473
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.211446
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2775
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2990.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4720.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4011.511139
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.462217408
X-RAY DIFFRACTIONr_scbond_it1.41936213
X-RAY DIFFRACTIONr_scangle_it1.6234.55432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4074 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.050.05
1Atight thermal0.10.5
2Btight thermal0.110.5
3Ctight thermal0.120.5
4Dtight thermal0.120.5
LS refinement shellResolution: 2.58→2.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 306 -
Rwork0.281 5531 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2144-0.50221.08830.9101-0.40912.2758-0.2302-0.7401-0.29160.07030.40190.3296-0.32-1.1985-0.1718-0.12060.27230.06840.53340.1821-0.0379-0.05559.37545.758
21.6766-0.19631.26470.9438-0.32342.6173-0.261-0.9284-0.13780.27760.40590.1845-0.377-1.1182-0.1449-0.0890.33510.12350.63170.1765-0.097621.43652.21274.663
31.3647-0.61230.56531.2483-0.54822.29770.1577-0.1155-0.3251-0.0956-0.020.02950.56240.1224-0.1377-0.09320.0976-0.0227-0.17670.0548-0.074746.16531.1449.138
41.402-0.69980.6350.956-0.45841.86470.16220.2301-0.0591-0.2074-0.10970.06480.1240.048-0.0525-0.13040.0866-0.0128-0.1812-0.0329-0.19432.08450.62121.247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 5553 - 555
2X-RAY DIFFRACTION2BB3 - 5553 - 555
3X-RAY DIFFRACTION3CC3 - 5553 - 555
4X-RAY DIFFRACTION4DD3 - 5553 - 555

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