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- PDB-7vb3: Crystal structure of hydroxynitrile lyase from Linum usitatissimum -

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Basic information

Entry
Database: PDB / ID: 7vb3
TitleCrystal structure of hydroxynitrile lyase from Linum usitatissimum
ComponentsAliphatic (R)-hydroxynitrile lyase
KeywordsLYASE / hydroxynitrile lyase / NAD
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aliphatic (R)-hydroxynitrile lyase
Similarity search - Component
Biological speciesLinum usitatissimum (flax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 16, 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)198,14243
Polymers192,6694
Non-polymers5,47439
Water30,0491668
1
A: Aliphatic (R)-hydroxynitrile lyase
B: Aliphatic (R)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,77028
Polymers96,3342
Non-polymers3,43626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-116 kcal/mol
Surface area29740 Å2
MethodPISA
2
C: Aliphatic (R)-hydroxynitrile lyase
D: Aliphatic (R)-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,37215
Polymers96,3342
Non-polymers2,03813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-134 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.120, 52.180, 168.510
Angle α, β, γ (deg.)90.000, 95.010, 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 , 7 types, 1707 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3 / 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.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: 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.: 3 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1668 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
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 mono methyl 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: 1.48→167.866 Å / Num. obs: 269690 / % possible obs: 99.6 % / Redundancy: 6.1 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Rsym value: 0.092 / Net I/av σ(I): 5.6 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.482-1.566.20.6611.1389640.2840.720.66199.2
1.56-1.665.90.4461.7369180.1980.4890.44699.4
1.66-1.776.10.3092.4347870.1340.3370.30999.5
1.77-1.916.10.2033.7325490.0880.2220.20399.7
1.91-2.15.90.1365.3299460.060.1490.13699.7
2.1-2.346.40.1036.7271730.0440.1120.10399.9
2.34-2.715.90.0818.1240600.0360.0890.081100
2.71-3.316.50.0679.1204310.0280.0730.067100
3.31-4.6960.05611.1159370.0240.0610.056100
4.69-85.0826.20.04611.689250.020.050.04699.9

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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: 1D1T

1d1t


Resolution: 1.48→84.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.307 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.183 13630 5.1 %RANDOM
Rwork0.156 ---
obs0.1574 255992 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.01 Å2 / Biso mean: 17.294 Å2 / Biso min: 8.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å20.11 Å2
2--0.81 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 1.48→84.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12462 0 332 1668 14462
Biso mean--22.48 27.65 -
Num. residues----1639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01313102
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712614
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.64717722
X-RAY DIFFRACTIONr_angle_other_deg1.5041.58229212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94151665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62323.66571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.681152278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3941555
X-RAY DIFFRACTIONr_chiral_restr0.10.21758
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022706
LS refinement shellResolution: 1.482→1.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 1053 -
Rwork0.244 18669 -
all-19722 -
obs--98.92 %

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