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- PDB-3x3h: Crystal Structure of the Manihot esculenta Hydroxynitrile Lyase (... -

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Basic information

Entry
Database: PDB / ID: 3x3h
TitleCrystal Structure of the Manihot esculenta Hydroxynitrile Lyase (MeHNL) 3KP (K176P, K199P, K224P) triple mutant
Components(S)-hydroxynitrile lyase
KeywordsLYASE / Hydroxynitrilase
Function / homology
Function and homology information


aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / (S)-hydroxynitrile lyase
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 / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsCielo, C.B.C. / Yamane, T. / Asano, Y. / Dadashipour, M. / Suzuki, A. / Mizushima, T. / Komeda, H. / Okazaki, S.
CitationJournal: TO BE PUBLISHED
Title: Crystallographic Studies of Manihot esculenta hydroxynitrile lyase Lysine-to-Proline mutants
Authors: Cielo, C.B.C. / Yamane, T. / Asano, Y. / Dadashipour, M. / Suzuki, A. / Mizushima, T. / Komeda, H. / Okazaki, S.
History
DepositionJan 21, 2015Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 2, 2016ID: 3RKT
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (S)-hydroxynitrile lyase
B: (S)-hydroxynitrile lyase
C: (S)-hydroxynitrile lyase
D: (S)-hydroxynitrile lyase
E: (S)-hydroxynitrile lyase
F: (S)-hydroxynitrile lyase
G: (S)-hydroxynitrile lyase
H: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)234,5008
Polymers234,5008
Non-polymers00
Water00
1
A: (S)-hydroxynitrile lyase
F: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)58,6252
Polymers58,6252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-13 kcal/mol
Surface area19060 Å2
MethodPISA
2
B: (S)-hydroxynitrile lyase
E: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)58,6252
Polymers58,6252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-13 kcal/mol
Surface area19090 Å2
MethodPISA
3
C: (S)-hydroxynitrile lyase
H: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)58,6252
Polymers58,6252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-13 kcal/mol
Surface area19110 Å2
MethodPISA
4
D: (S)-hydroxynitrile lyase
G: (S)-hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)58,6252
Polymers58,6252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-14 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.040, 84.210, 134.900
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

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
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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


Mass: 29312.488 Da / Num. of mol.: 8 / Mutation: K176P, K199P, K224P
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

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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: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25%(v/v) PEG 3350, 0.1M Tris/HCl (pH 8.5), 0.2M Ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 11, 2010
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.88→100 Å / Num. obs: 41899 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
REFMAC5.7.0029refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DWP

1dwp


Resolution: 2.88→15.26 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 16.684 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23785 2100 5 %RANDOM
Rwork0.20427 ---
all0.20597 41899 --
obs0.20597 39489 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2---0.11 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.88→15.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16544 0 0 0 16544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916976
X-RAY DIFFRACTIONr_bond_other_d0.0070.0216112
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9523080
X-RAY DIFFRACTIONr_angle_other_deg1.44337152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37652056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56624.536776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.869152872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7431564
X-RAY DIFFRACTIONr_chiral_restr0.0850.22568
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02119016
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023880
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A171230.06
12B171230.06
21A171120.07
22C171120.07
31A170900.06
32D170900.06
41A169450.07
42E169450.07
51A168880.07
52F168880.07
61A169970.07
62G169970.07
71A168740.07
72H168740.07
81B170760.07
82C170760.07
91B169610.07
92D169610.07
101B169080.08
102E169080.08
111B168210.08
112F168210.08
121B169020.08
122G169020.08
131B167690.08
132H167690.08
141C170150.07
142D170150.07
151C168250.08
152E168250.08
161C168330.08
162F168330.08
171C169040.07
172G169040.07
181C167870.08
182H167870.08
191D167710.08
192E167710.08
201D168200.08
202F168200.08
211D168860.07
212G168860.07
221D167770.08
222H167770.08
231E168410.08
232F168410.08
241E169790.07
242G169790.07
251E168420.08
252H168420.08
261F171220.06
262G171220.06
271F167890.08
272H167890.08
281G168620.07
282H168620.07
LS refinement shellResolution: 2.882→2.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 105 -
Rwork0.309 2183 -
obs--73.55 %

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