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- PDB-4mnl: Crystal Structure of GH18 Chitinase (G77W/E119Q mutant) from Cyca... -

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Basic information

Entry
Database: PDB / ID: 4mnl
TitleCrystal Structure of GH18 Chitinase (G77W/E119Q mutant) from Cycas revoluta in complex with (GlcNAc)4
ComponentsChitinase A
KeywordsHYDROLASE / Chitinase / Carbohydrate
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
ACETATE ION / Chitinase A
Similarity search - Component
Biological speciesCycas revoluta (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsUmemoto, N. / Numata, T. / Ohnuma, T. / Osawa, T. / Taira, T. / Fukamizo, T.
CitationJournal: To be Published
Title: Crystal Structure of GH18 Chitinase form Cycad, Cycas revoluta
Authors: Umemoto, N. / Numata, T. / Ohnuma, T. / Osawa, T. / Taira, T. / Fukamizo, T.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2714
Polymers38,7291
Non-polymers5423
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.478, 64.109, 85.838
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: 38728.621 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-370 / Mutation: G77W, E119Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cycas revoluta (plant) / Gene: crchiA / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4W6L6, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% v/v Tacsimate pH 7.0, 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 4, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→51.36 Å / Num. obs: 42641 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 58.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 10.8 / Num. unique all: 21984 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ALF

3alf


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.695 / SU ML: 0.061 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2142 5 %RANDOM
Rwork0.19852 ---
obs0.19951 40438 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.517 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2---0.54 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 37 270 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222817
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.9573836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.72623.488129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3731517
X-RAY DIFFRACTIONr_chiral_restr0.0740.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212190
X-RAY DIFFRACTIONr_mcbond_it0.4291.51715
X-RAY DIFFRACTIONr_mcangle_it0.82922751
X-RAY DIFFRACTIONr_scbond_it1.27231102
X-RAY DIFFRACTIONr_scangle_it2.1484.51085
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 176 -
Rwork0.253 2832 -
obs--97.22 %

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