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- PDB-9clr: Hydroxynitrile Lyase from Hevea brasiliensis with Seventy-one Mut... -

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Entry
Database: PDB / ID: 9clr
TitleHydroxynitrile Lyase from Hevea brasiliensis with Seventy-one Mutations
ComponentsSeventy-one-substitution variants of hydroxynitrile lyase
KeywordsHYDROLASE / Engineered Protein / esterase
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsTan, P. / Meixner, E.L. / Nguyen, A. / Kazlaukas, R.J. / Pierce, C.T. / Evans, R.L. / Shi, K. / Aihara, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2039039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS R35-GM118047 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree.
Authors: Pierce, C.T. / Tan, P. / Greenberg, L.R. / Walsh, M.E. / Shi, K. / Nguyen, A.H. / Meixner, E.L. / Sarak, S. / Aihara, H. / Evans 3rd, R.L. / Kazlauskas, R.J.
History
DepositionJul 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Seventy-one-substitution variants of hydroxynitrile lyase
B: Seventy-one-substitution variants of hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1739
Polymers60,9242
Non-polymers2497
Water1,06359
1
A: Seventy-one-substitution variants of hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6034
Polymers30,4621
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Seventy-one-substitution variants of hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5705
Polymers30,4621
Non-polymers1084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.966, 80.751, 135.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Seventy-one-substitution variants of hydroxynitrile lyase


Mass: 30462.018 Da / Num. of mol.: 2
Mutation: I9V, T11G, I12A, I18S, E79H, C81L, L84M, H103L, N104A, S105A, V106F, V118L, L121Y, M122N, F125T, D127N, Y133F, L146M, K147F, L148F, L152F, N156K, T173V, G176S, Q180M, E208K, I209G, F210I, ...Mutation: I9V, T11G, I12A, I18S, E79H, C81L, L84M, H103L, N104A, S105A, V106F, V118L, L121Y, M122N, F125T, D127N, Y133F, L146M, K147F, L148F, L152F, N156K, T173V, G176S, Q180M, E208K, I209G, F210I, L211P, K236M, L237A, and Q238M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M magnesium chloride hexahydrate, 25% w/v Polyethylene glycol 3,350
PH range: 8.35-8.60

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→42.49 Å / Num. obs: 36436 / % possible obs: 94.64 % / Redundancy: 5.98 % / Biso Wilson estimate: 26.87 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.995 / Rpim(I) all: 0.066 / Rrim(I) all: 0.183 / Net I/σ(I): 7.6
Reflection shellResolution: 1.99→2.061 Å / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3148 / CC1/2: 0.804 / Rpim(I) all: 0.342 / Rrim(I) all: 0.943 / % possible all: 83.36

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→42.49 Å / SU ML: 0.3042 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2532 1815 4.98 %
Rwork0.22 34621 -
obs0.2217 36436 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.19 Å2
Refinement stepCycle: LAST / Resolution: 1.99→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 12 59 3794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683828
X-RAY DIFFRACTIONf_angle_d0.89875195
X-RAY DIFFRACTIONf_chiral_restr0.05577
X-RAY DIFFRACTIONf_plane_restr0.0058654
X-RAY DIFFRACTIONf_dihedral_angle_d11.9425523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.3341360.3262575X-RAY DIFFRACTION93.42
2.04-2.10.32581290.30642224X-RAY DIFFRACTION80.25
2.1-2.170.36441520.29412754X-RAY DIFFRACTION99.35
2.17-2.250.38151220.28462389X-RAY DIFFRACTION86.53
2.25-2.340.31891410.25982753X-RAY DIFFRACTION99.59
2.34-2.440.32871450.24552795X-RAY DIFFRACTION99.97
2.44-2.570.28311250.22882805X-RAY DIFFRACTION99.83
2.57-2.730.26721460.21992500X-RAY DIFFRACTION89.88
2.73-2.950.26181490.23262808X-RAY DIFFRACTION99.86
2.95-3.240.26351560.22522799X-RAY DIFFRACTION99.76
3.24-3.710.25311230.21492467X-RAY DIFFRACTION87.03
3.71-4.670.18911390.16372732X-RAY DIFFRACTION94.78
4.68-42.490.19031520.19123020X-RAY DIFFRACTION99.91

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