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- PDB-6kfb: Hydroxynitrile lyase from the millipede, Chamberlinius hualienens... -

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Basic information

Entry
Database: PDB / ID: 6kfb
TitleHydroxynitrile lyase from the millipede, Chamberlinius hualienensis bound with thiocyanate
ComponentsHydroxynitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / lipocalin fold / four disulfide bonds / dimer
Function / homologyRicin B-like lectins / lyase activity / THIOCYANATE ION / Hydroxynitrile lyase
Function and homology information
Biological speciesChamberlinius hualienensis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMotojima, F. / Izumi, A. / Asano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER1102 Japan
CitationJournal: Febs J. / Year: 2021
Title: R-hydroxynitrile lyase from the cyanogenic millipede, Chamberlinius hualienensis-A new entry to the carrier protein family Lipocalines.
Authors: Motojima, F. / Izumi, A. / Nuylert, A. / Zhai, Z. / Dadashipour, M. / Shichida, S. / Yamaguchi, T. / Nakano, S. / Asano, Y.
History
DepositionJul 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 23, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 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
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6673
Polymers18,2411
Non-polymers4252
Water4,089227
1
A: Hydroxynitrile lyase
hetero molecules

A: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3336
Polymers36,4832
Non-polymers8514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area4830 Å2
ΔGint-19 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.095, 58.095, 225.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Hydroxynitrile lyase


Mass: 18241.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chamberlinius hualienensis (arthropod) / References: UniProt: A0A0H5BR52
#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.06 Å3/Da / Density % sol: 59.83 % / Description: BIPYRAMID
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE (PH 5.0), 28-32% (W/V) PEG MONOMETHYL ETHER 2000, 0.3 M NDSB-195, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 20, 2016
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→49.11 Å / Num. obs: 34043 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 18.7 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 34.7
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 16.9 / Num. unique obs: 4801 / CC1/2: 0.974 / Rpim(I) all: 0.133 / Rrim(I) all: 0.552 / Rsym value: 0.552 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDS0.48data reduction
SCALA3.3.22data scaling
MOLREP11.2.08phasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KFA

6kfa


Resolution: 1.55→49.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.013 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1722 5.1 %RANDOM
Rwork0.17 ---
obs0.171 32225 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.55→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 27 227 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191389
X-RAY DIFFRACTIONr_bond_other_d0.0020.021168
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9561902
X-RAY DIFFRACTIONr_angle_other_deg0.90632749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4295171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88425.65269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03815214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.128153
X-RAY DIFFRACTIONr_chiral_restr0.0790.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211565
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02269
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_it0.7281.72668
X-RAY DIFFRACTIONr_mcbond_other0.7281.718665
X-RAY DIFFRACTIONr_mcangle_it1.1832.578837
X-RAY DIFFRACTIONr_mcangle_other1.1822.578838
X-RAY DIFFRACTIONr_scbond_it1.261.95721
X-RAY DIFFRACTIONr_scbond_other1.261.95721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9872.881064
X-RAY DIFFRACTIONr_long_range_B_refined4.54223.2181615
X-RAY DIFFRACTIONr_long_range_B_other4.12621.6871540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 131 -
Rwork0.244 2277 -
obs--99.09 %

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