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- PDB-3wwp: S-selective hydroxynitrile lyase from Baliospermum montanum (apo2) -

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Basic information

Entry
Database: PDB / ID: 3wwp
TitleS-selective hydroxynitrile lyase from Baliospermum montanum (apo2)
Components(S)-hydroxynitrile lyase(S)-hydroxynitrile lyase
KeywordsLYASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesBaliospermum montanum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakano, S. / Dadashipour, M. / Asano, Y.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
Authors: Nakano, S. / Dadashipour, M. / Asano, Y.
History
DepositionJun 23, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: (S)-hydroxynitrile lyase
B: (S)-hydroxynitrile lyase
G: (S)-hydroxynitrile lyase
L: (S)-hydroxynitrile lyase
M: (S)-hydroxynitrile lyase
R: (S)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,36855
Polymers195,0946
Non-polymers4,27449
Water33,3101849
1
A: (S)-hydroxynitrile lyase
B: (S)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,75122
Polymers65,0312
Non-polymers1,72020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-98 kcal/mol
Surface area20680 Å2
MethodPISA
2
G: (S)-hydroxynitrile lyase
L: (S)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,43518
Polymers65,0312
Non-polymers1,40416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-88 kcal/mol
Surface area20300 Å2
MethodPISA
3
M: (S)-hydroxynitrile lyase
R: (S)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,18115
Polymers65,0312
Non-polymers1,15013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-52 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.962, 261.581, 91.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21L-499-

HOH

31L-617-

HOH

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Components

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Protein , 1 types, 6 molecules ABGLMR

#1: Protein
(S)-hydroxynitrile lyase / (S)-hydroxynitrile lyase


Mass: 32515.619 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Baliospermum montanum (plant) / Gene: bmhnl / Production host: Escherichia coli (E. coli) / References: UniProt: D1MX73

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Non-polymers , 5 types, 1898 molecules

#2: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1849 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.0M Lithium sulfate, 0.1M sodium citrate, 0.5M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→45.99 Å / Num. all: 181408 / Num. obs: 181227 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.93 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.514 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19858 9074 5 %RANDOM
Rwork0.1595 ---
obs0.16144 172073 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.638 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12464 0 250 1849 14563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912983
X-RAY DIFFRACTIONr_bond_other_d00.0212029
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.95717632
X-RAY DIFFRACTIONr_angle_other_deg0.739327723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69351562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9725.098612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26152090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3451536
X-RAY DIFFRACTIONr_chiral_restr0.2310.21942
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02114624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022972
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 679 -
Rwork0.248 12564 -
obs--99.59 %

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