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- PDB-7bow: Hydroxynitrile lyase from Parafonteria laminate -

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Basic information

Entry
Database: PDB / ID: 7bow
TitleHydroxynitrile lyase from Parafonteria laminate
ComponentsHydroxynitrile lyase
KeywordsLYASE / hydroxynitrile lyase / millipede
Biological speciesParafontaria falcifera (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsNuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER1102 Japan
Japan Society for the Promotion of Science (JSPS)17H06169 Japan
CitationJournal: To Be Published
Title: Hydroxynitrile lyase from Parafonteria laminate
Authors: Nuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y.
History
DepositionMar 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5454
Polymers36,3612
Non-polymers1842
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-28 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.236, 33.153, 72.067
Angle α, β, γ (deg.)90.000, 106.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hydroxynitrile lyase


Mass: 18180.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parafontaria falcifera (arthropod) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: potassium thiocyanate, sodium acetate PEG 8000, PEG 1000

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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: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→69.196 Å / Num. all: 59066 / Num. obs: 59066 / % possible obs: 100 % / Redundancy: 6.6 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Rsym value: 0.081 / Net I/av σ(I): 4.9 / Net I/σ(I): 12 / Num. measured all: 390845
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.42-1.56.50.7915563485510.3330.8590.792.2100
1.5-1.596.60.4991.55361181380.2090.5420.4993.5100
1.59-1.76.60.3212.45035875760.1340.3490.3215.3100
1.7-1.836.80.1953.84816271270.0810.2120.1958.3100
1.83-2.016.50.1255.74261965410.0530.1360.12512.1100
2.01-2.256.80.097.54047059270.0370.0980.0917.199.9
2.25-2.596.50.0728.63442852600.030.0780.07220.799.9
2.59-3.186.80.0619.33038244630.0260.0670.06125.4100
3.18-4.496.50.0569.72261635010.0240.0610.05629.699.9
4.49-34.8836.30.0539.51256519820.0230.0580.05328.999.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JHC

6jhc


Resolution: 1.42→34.91 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1803 / WRfactor Rwork: 0.1555 / FOM work R set: 0.9189 / SU B: 0.669 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0575 / SU Rfree: 0.0596 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 2975 5 %RANDOM
Rwork0.1523 ---
obs0.1535 56079 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.09 Å2 / Biso mean: 16.941 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.42→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 12 430 2996
Biso mean--37.92 32.32 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172292
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6563652
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5735367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02424.409127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08615384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.228155
X-RAY DIFFRACTIONr_chiral_restr0.0650.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.13 249 -
Rwork0.126 4071 -
all-4320 -
obs--99.82 %

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