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- PDB-7vb5: Crystal structure of hydroxynitrile lyase from Linum usitatissimu... -

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Basic information

Entry
Database: PDB / ID: 7vb5
TitleCrystal structure of hydroxynitrile lyase from Linum usitatissimum complexed with acetone cyanohydrin
ComponentsAliphatic (R)-hydroxynitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / NAD / ZN / CNH
Function / homology
Function and homology information


aliphatic (R)-hydroxynitrile lyase / aliphatic (R)-hydroxynitrile lyase activity / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETONE / 2-HYDROXY-2-METHYLPROPANENITRILE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aliphatic (R)-hydroxynitrile lyase
Similarity search - Component
Biological speciesLinum usitatissimum (flax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZheng, D. / Nakabayashi, M. / Asano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex.
Authors: Zheng, D. / Nakabayashi, M. / Asano, Y.
History
DepositionAug 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aliphatic (R)-hydroxynitrile lyase
B: Aliphatic (R)-hydroxynitrile lyase
C: Aliphatic (R)-hydroxynitrile lyase
D: Aliphatic (R)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,87359
Polymers192,6694
Non-polymers6,20455
Water20,4831137
1
A: Aliphatic (R)-hydroxynitrile lyase
B: Aliphatic (R)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,51043
Polymers96,3342
Non-polymers4,17641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-67 kcal/mol
Surface area30600 Å2
MethodPISA
2
C: Aliphatic (R)-hydroxynitrile lyase
D: Aliphatic (R)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,36316
Polymers96,3342
Non-polymers2,02914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-120 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.120, 51.570, 170.000
Angle α, β, γ (deg.)90.000, 94.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aliphatic (R)-hydroxynitrile lyase / LuHNL


Mass: 48167.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Linum usitatissimum (flax) / Production host: Escherichia coli (E. coli)
References: UniProt: P93243, aliphatic (R)-hydroxynitrile lyase

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Non-polymers , 9 types, 1192 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CNH / 2-HYDROXY-2-METHYLPROPANENITRILE / ACETONE CYANOHYDRIN


Mass: 85.104 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#9: Chemical ChemComp-ACN / ACETONE


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS, pH 6.5, 20% w/v polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→169.436 Å / Num. all: 223351 / Num. obs: 223351 / % possible obs: 100 % / Redundancy: 6.2 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.133 / Rsym value: 0.121 / Net I/av σ(I): 4.9 / Net I/σ(I): 8.9 / Num. measured all: 1381304
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.58-1.676.31.3230.6203937324710.5681.4431.3231.3100
1.67-1.7760.8760.9183868306570.3860.9590.8761.999.9
1.77-1.896.10.5341.4176926288440.2320.5840.5343.199.9
1.89-2.046.30.332.3168834268690.1410.360.335100
2.04-2.235.90.1963.8146142248560.0880.2160.1967.6100
2.23-2.56.50.1335.6145060223800.0560.1440.13311.2100
2.5-2.8860.0917.8119241198850.040.10.09114.5100
2.88-3.536.60.06310.4111780168350.0260.0680.06322100
3.53-56.10.05211.179511131390.0230.0570.05227.2100
5-93.8086.20.0539.34600574150.0220.0570.05326.8100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
Cootmodel building
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VB3

7vb3


Resolution: 1.58→93.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.437 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 11126 5 %RANDOM
Rwork0.1706 ---
obs0.1722 212183 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 23.96 Å2 / Biso min: 9.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20.78 Å2
2--1.5 Å20 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 1.58→93.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12532 0 380 1137 14049
Biso mean--30.52 31.25 -
Num. residues----1648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01313281
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712853
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6517951
X-RAY DIFFRACTIONr_angle_other_deg1.381.58229753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13451694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59823.481586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.012152314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1171560
X-RAY DIFFRACTIONr_chiral_restr0.0810.21779
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022751
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 846 -
Rwork0.339 15654 -
all-16500 -
obs--99.99 %

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