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- PDB-4r5e: Crystal Structure of Family GH18 Chitinase from Cycas revoluta a ... -

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Basic information

Entry
Database: PDB / ID: 4r5e
TitleCrystal Structure of Family GH18 Chitinase from Cycas revoluta a Complex with Allosamidin
ComponentsChitinase A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Chitinase / Carbohydrate / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases ...Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Allosamidin / ACETATE ION / ALLOSAMIZOLINE / Chitinase A
Similarity search - Component
Biological speciesCycas revoluta (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUmemoto, N. / Numata, T. / Ohnuma, T. / Fukamizo, T.
CitationJournal: Plant J. / Year: 2015
Title: Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features.
Authors: Umemoto, N. / Kanda, Y. / Ohnuma, T. / Osawa, T. / Numata, T. / Sakuda, S. / Taira, T. / Fukamizo, T.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 2.0Apr 13, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / 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_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq_dif.details
Revision 2.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3595
Polymers38,6001
Non-polymers7594
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.842, 64.114, 85.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase A


Mass: 38600.449 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cycas revoluta (plant) / Gene: crchiA / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4W6L6, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: Allosamidin
DescriptorTypeProgram
DAllpNAcb1-4DAllpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2222h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-AllpNAc]{[(4+1)][b-D-AllpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-AMI / ALLOSAMIZOLINE


Type: Oligosaccharide / Class: Inhibitor / Mass: 216.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N2O4 / References: Allosamidin
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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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: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% V/V TACSIMATE pH 7.0, 0.1M BIS-TRIS PROPANE pH 7.0, 0.06MM ALLOSAMIDIN, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromater, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→51.31 Å / Num. obs: 51423 / % possible obs: 99.3 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 52.16
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 8.6 / Num. unique all: 22732 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ALF

3alf


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.239 / SU ML: 0.047 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19414 2610 5.1 %RANDOM
Rwork0.18134 ---
obs0.182 48750 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.749 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-0 Å2
2---0.55 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 51 261 2991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192838
X-RAY DIFFRACTIONr_bond_other_d0.0010.022629
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9653870
X-RAY DIFFRACTIONr_angle_other_deg0.75836047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3845349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92323.571126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56815420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9041516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213239
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
X-RAY DIFFRACTIONr_mcbond_it0.5041.2031392
X-RAY DIFFRACTIONr_mcbond_other0.5021.2021389
X-RAY DIFFRACTIONr_mcangle_it0.91.81741
X-RAY DIFFRACTIONr_mcangle_other0.91.81742
X-RAY DIFFRACTIONr_scbond_it0.6331.291446
X-RAY DIFFRACTIONr_scbond_other0.6331.291447
X-RAY DIFFRACTIONr_scangle_other1.0421.912130
X-RAY DIFFRACTIONr_long_range_B_refined2.80710.6123517
X-RAY DIFFRACTIONr_long_range_B_other2.62810.2733400
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 185 -
Rwork0.211 3470 -
obs--96.82 %

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