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

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Basic information

Entry
Database: PDB / ID: 6kfa
TitleHydroxynitrile lyase from the millipede, Chamberlinius hualienensis bound with acetate
ComponentsHydroxynitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / lipocalin fold / four disulfide bonds / dimer
Function / homologyRicin B-like lectins / lyase activity / ACETATE ION / Hydroxynitrile lyase
Function and homology information
Biological speciesChamberlinius hualienensis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jun 23, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
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

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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)18,7434
Polymers18,2411
Non-polymers5013
Water5,441302
1
A: Hydroxynitrile lyase
hetero molecules

A: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4858
Polymers36,4832
Non-polymers1,0036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area4600 Å2
ΔGint-17 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.247, 58.247, 224.978
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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 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 Å / Relative weight: 1
ReflectionResolution: 1.5→50.44 Å / Num. obs: 35572 / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 9.5 / Num. unique obs: 4460 / CC1/2: 0.989 / Rpim(I) all: 0.073 / Rrim(I) all: 0.229 / Rsym value: 0.251 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS0.48data reduction
SCALA3.3.22data scaling
SHELXCD2015/2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→50.44 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.114 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18686 1843 4.9 %RANDOM
Rwork0.17392 ---
obs0.17456 35572 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 32 305 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191390
X-RAY DIFFRACTIONr_bond_other_d0.0020.021167
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.961906
X-RAY DIFFRACTIONr_angle_other_deg0.90332745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76625.65269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.068153
X-RAY DIFFRACTIONr_chiral_restr0.0750.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211579
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
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_it0.7051.606667
X-RAY DIFFRACTIONr_mcbond_other0.7051.605665
X-RAY DIFFRACTIONr_mcangle_it1.1462.411837
X-RAY DIFFRACTIONr_mcangle_other1.1462.411838
X-RAY DIFFRACTIONr_scbond_it1.2211.807723
X-RAY DIFFRACTIONr_scbond_other1.221.811724
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9642.6691068
X-RAY DIFFRACTIONr_long_range_B_refined4.85422.6361682
X-RAY DIFFRACTIONr_long_range_B_other4.40320.4771571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 148 -
Rwork0.281 2555 -
obs--99.93 %

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