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- PDB-4yk7: Crystal structure of S-hydroxynitrile lyase from Manihot esculent... -

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Basic information

Entry
Database: PDB / ID: 4yk7
TitleCrystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu)
Components(S)-hydroxynitrile lyase
KeywordsLYASE / S-hydroxynitrile lyase / hydrolase fold / His103Leu variant
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity
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
(S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesManihot esculenta (cassava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsDadashipour, M. / Nakano, S. / Asano, Y.
CitationJournal: To Be Published
Title: Crystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu)
Authors: Dadashipour, M. / Nakano, S. / Asano, Y.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: (S)-hydroxynitrile lyase
D: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)117,5354
Polymers117,5354
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: (S)-hydroxynitrile lyase
B: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)58,7672
Polymers58,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14 kcal/mol
Surface area19230 Å2
MethodPISA
3
C: (S)-hydroxynitrile lyase
D: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)58,7672
Polymers58,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-15 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.469, 88.098, 135.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 258 / Label seq-ID: 1 - 258

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
(S)-hydroxynitrile lyase / (S)-acetone-cyanohydrin lyase / Oxynitrilase


Mass: 29383.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manihot esculenta (cassava) / Gene: HNL / Production host: Escherichia coli (E. coli) / References: UniProt: P52705, (S)-hydroxynitrile lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.1M DL-Maleic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→45.6 Å / Num. obs: 32186 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 34.6
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 12.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.6→45.6 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.84 / SU B: 11.329 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26226 1631 5.1 %RANDOM
Rwork0.23995 ---
obs0.24107 30495 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.999 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å2-0 Å20 Å2
2--5.47 Å2-0 Å2
3----3.11 Å2
Refinement stepCycle: 1 / Resolution: 2.6→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8288 0 0 60 8348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198488
X-RAY DIFFRACTIONr_bond_other_d0.0030.028140
X-RAY DIFFRACTIONr_angle_refined_deg1.011.95211512
X-RAY DIFFRACTIONr_angle_other_deg0.781318760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30651028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91124.583384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.393151488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.981532
X-RAY DIFFRACTIONr_chiral_restr0.0640.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219472
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021936
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A166280.09
12B166280.09
21A170610.07
22C170610.07
31A166500.09
32D166500.09
41B165780.1
42C165780.1
51B171190.07
52D171190.07
61C165250.1
62D165250.1
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 99 -
Rwork0.271 2014 -
obs--90.49 %

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