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- PDB-5y02: C-terminal peptide depleted mutant of hydroxynitrile lyase from P... -

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Basic information

Entry
Database: PDB / ID: 5y02
TitleC-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile
ComponentsHydroxynitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / Cyanohydrins
Function / homology
Function and homology information


pollen tube adhesion / lyase activity
Similarity search - Function
Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
benzaldehyde / HEXANE-1,6-DIOL / (2R)-hydroxy(phenyl)ethanenitrile / Hydroxynitrile lyase
Similarity search - Component
Biological speciesPassiflora edulis (passion fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMotojima, F. / Nuylert, A. / Asano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSTJPMJER1102 Japan
CitationJournal: FEBS J. / Year: 2018
Title: The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis
Authors: Motojima, F. / Nuylert, A. / Asano, Y.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.4May 16, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxynitrile lyase
B: Hydroxynitrile lyase
C: Hydroxynitrile lyase
D: Hydroxynitrile lyase
E: Hydroxynitrile lyase
F: Hydroxynitrile lyase
G: Hydroxynitrile lyase
H: Hydroxynitrile lyase
I: Hydroxynitrile lyase
J: Hydroxynitrile lyase
K: Hydroxynitrile lyase
L: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,05427
Polymers148,24612
Non-polymers1,80815
Water26,0501446
1
A: Hydroxynitrile lyase
B: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9594
Polymers24,7082
Non-polymers2512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-12 kcal/mol
Surface area10480 Å2
MethodPISA
2
C: Hydroxynitrile lyase
D: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9594
Polymers24,7082
Non-polymers2512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-15 kcal/mol
Surface area10460 Å2
MethodPISA
3
E: Hydroxynitrile lyase
F: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0775
Polymers24,7082
Non-polymers3693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-16 kcal/mol
Surface area9850 Å2
MethodPISA
4
G: Hydroxynitrile lyase
H: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9444
Polymers24,7082
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-9 kcal/mol
Surface area10180 Å2
MethodPISA
5
I: Hydroxynitrile lyase
J: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0505
Polymers24,7082
Non-polymers3423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-12 kcal/mol
Surface area10510 Å2
MethodPISA
6
K: Hydroxynitrile lyase
L: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0655
Polymers24,7082
Non-polymers3573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-18 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.811, 88.494, 104.454
Angle α, β, γ (deg.)90.00, 105.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hydroxynitrile lyase


Mass: 12353.840 Da / Num. of mol.: 12 / Fragment: UNP residues 27-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Passiflora edulis (passion fruit) / Tissue: leave / Gene: PeHNL / Plasmid: pET21 / Details (production host): MBP fusion / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1L7NZN4
#2: Chemical
ChemComp-MXN / (2R)-hydroxy(phenyl)ethanenitrile / (R)-mandelonitrile


Mass: 133.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-HBX / benzaldehyde / Benzaldehyde


Mass: 106.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1446 / 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: 2.56 Å3/Da / Density % sol: 51.95 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% (w/v) PEG3350 2.1% (w/v) 1,6-hexanediol 150 mM NaCl 50 mM HEPES-NaOH, pH 7.0
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 19, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.12 Å / Num. obs: 135483 / % possible obs: 97.2 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.03 / Rrim(I) all: 0.03 / Rsym value: 0.071 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 106710 / CC1/2: 0.863 / Rpim(I) all: 0.254 / Rrim(I) all: 0.254 / Rsym value: 0.603 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XZT

5xzt


Resolution: 1.8→49.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.901 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21477 6683 4.9 %RANDOM
Rwork0.18088 ---
obs0.18253 128774 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.468 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20.1 Å2
2---0.07 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10303 0 128 1446 11877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910906
X-RAY DIFFRACTIONr_bond_other_d0.0020.029659
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.93714802
X-RAY DIFFRACTIONr_angle_other_deg0.891322505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24651282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85624.783598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69151722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1261540
X-RAY DIFFRACTIONr_chiral_restr0.0850.21517
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022400
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_it1.6012.5485036
X-RAY DIFFRACTIONr_mcbond_other1.5992.5485035
X-RAY DIFFRACTIONr_mcangle_it2.6633.8026284
X-RAY DIFFRACTIONr_mcangle_other2.6633.8026285
X-RAY DIFFRACTIONr_scbond_it1.7732.8325870
X-RAY DIFFRACTIONr_scbond_other1.7722.8325870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.944.1528497
X-RAY DIFFRACTIONr_long_range_B_refined5.49831.53113229
X-RAY DIFFRACTIONr_long_range_B_other5.20730.59312714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 494 -
Rwork0.294 9314 -
obs--95.4 %

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