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

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Basic information

Entry
Database: PDB / ID: 4mnm
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 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesCycas revoluta (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUmemoto, N. / Numata, T. / Ohnuma, T. / Osawa, T. / Taira, T. / Fukamizo, T.
CitationJournal: To be Published
Title: Crystal Structure of GH18 Chitinase from 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 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 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)39,3967
Polymers38,7291
Non-polymers6686
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.540, 64.500, 86.024
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01M Magnesium sulfate heptahydrate, 0.05M Sodium cacodylate trihydrate pH 6.5, 2.0M Ammonium sulfate, 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 23, 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: 1.8→51.61 Å / Num. obs: 30778 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 43.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 10.6 / Num. unique all: 10829 / % possible all: 99.7

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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: 1.8→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.532 / SU ML: 0.081 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21677 1545 5 %RANDOM
Rwork0.19067 ---
obs0.19197 29182 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.451 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2---1.03 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 39 192 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222845
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9553879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1835349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18823.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66715428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8831518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212210
X-RAY DIFFRACTIONr_mcbond_it0.4551.51732
X-RAY DIFFRACTIONr_mcangle_it0.86322786
X-RAY DIFFRACTIONr_scbond_it1.38531113
X-RAY DIFFRACTIONr_scangle_it2.3374.51093
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 119 -
Rwork0.227 2085 -
obs--98.92 %

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