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- PDB-3hbe: Class IV chitinase structure from Picea abies at 1.55A -

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Basic information

Entry
Database: PDB / ID: 3hbe
TitleClass IV chitinase structure from Picea abies at 1.55A
ComponentsClass IV chitinase Chia4-Pa2
KeywordsHYDROLASE / endochitinase / chitinase / class IV / family 19 / conformational changes / Chitin-binding / Glycosidase
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / cell wall macromolecule catabolic process / carbohydrate metabolic process
Similarity search - Function
Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. ...Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMYL GROUP / 2-METHOXYETHANOL / Class IV chitinase Chia4-Pa2
Similarity search - Component
Biological speciesPicea abies (Norway spruce)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFMAC 5.2.0019 rigidbody refinement / Resolution: 1.55 Å
AuthorsUbhayasekera, W. / Mowbray, S.L.
CitationJournal: Plant Mol.Biol. / Year: 2009
Title: The first crystal structures of a family 19 class IV chitinase: the enzyme from Norway spruce.
Authors: Ubhayasekera, W. / Rawat, R. / Ho, S.W. / Wiweger, M. / Von Arnold, S. / Chye, M.L. / Mowbray, S.L.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Class IV chitinase Chia4-Pa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6974
Polymers21,5321
Non-polymers1653
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.194, 65.792, 36.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Class IV chitinase Chia4-Pa2


Mass: 21531.814 Da / Num. of mol.: 1 / Fragment: Catalytic module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Picea abies (Norway spruce) / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / References: UniProt: Q6WSR8, chitinase
#2: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.87 Å3/Da / Density % sol: 34.34 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% w/v polyethylene glycol 3000, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 23744 / % possible obs: 97.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.7
Reflection shellResolution: 1.55→1.63 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 6.3 / % possible all: 92.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.2.0019 rigidbody refinementrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019 rigidbody refinementphasing
RefinementMethod to determine structure: REFMAC 5.2.0019 rigidbody refinement
Starting model: Structure of Picea abies chitinase (PDB entry 3HBD)

3hbd


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.347 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19382 1202 5.1 %RANDOM
Rwork0.16261 ---
obs0.16419 22318 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 11 226 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221628
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.922215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2985224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8442570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90315251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.297153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021277
X-RAY DIFFRACTIONr_nbd_refined0.2040.2830
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.229
X-RAY DIFFRACTIONr_mcbond_it0.7171.51055
X-RAY DIFFRACTIONr_mcangle_it1.14421656
X-RAY DIFFRACTIONr_scbond_it1.9093660
X-RAY DIFFRACTIONr_scangle_it2.944.5547
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 78 -
Rwork0.192 1465 -
obs--86.78 %

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