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- PDB-4mpi: Crystal structure of the chitin-binding module (CBM18) of a chiti... -

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Basic information

Entry
Database: PDB / ID: 4mpi
TitleCrystal structure of the chitin-binding module (CBM18) of a chitinase-like protein from Hevea brasiliensis
ComponentsClass I chitinase
KeywordsSUGAR BINDING PROTEIN / hevein-like domain / chitin oligomers
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / defense response to fungus / cell wall macromolecule catabolic process / carbohydrate metabolic process
Similarity search - Function
Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase-like / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin recognition protein / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 ...Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase-like / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Chitin recognition protein / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Lysozyme-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Probable inactive chitinase-like protein LaCIC
Similarity search - Component
Biological speciesHevea brasiliensis subsp. brasiliensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsMartinez-Caballero, C.S. / Hermoso, J.A. / Rodriguez-Romero, A.
CitationJournal: Febs J. / Year: 2014
Title: Comparative study of two GH19 chitinase-like proteins from Hevea brasiliensis, one exhibiting a novel carbohydrate-binding domain.
Authors: Martinez-Caballero, S. / Cano-Sanchez, P. / Mares-Mejia, I. / Diaz-Sanchez, A.G. / Macias-Rubalcava, M.L. / Hermoso, J.A. / Rodriguez-Romero, A.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class I chitinase
B: Class I chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3014
Polymers9,0182
Non-polymers2832
Water1,53185
1
A: Class I chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7042
Polymers4,5091
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Class I chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5972
Polymers4,5091
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.515, 38.515, 100.934
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein/peptide Class I chitinase / chitinase-like lectin


Mass: 4509.008 Da / Num. of mol.: 2 / Fragment: Chitin-binding domain (CBD18, UNP residues 1-43)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis subsp. brasiliensis (plant)
Strain: RIMM600 / Tissue: latex and leaves / Gene: Hbchi-L1, laCIC / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami DE3 pLysS / References: UniProt: Q8GUD7
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 11 mg/mL protein, 0.1 M MES, pH 7.0, 1.6 M ammonium sulfate, 4% 1,4-dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012
RadiationMonochromator: liquid nitrogen cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.602→33.355 Å / Num. all: 11176 / Num. obs: 11117 / % possible obs: 99.47 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 12.65 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 21.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.602-1.682.70.2164.915000.21699.5
1.68-1.793.70.1787.515450.17899.9
1.79-1.913.60.10910.914420.10999.9
1.91-2.063.60.07415.613530.07499.9
2.06-2.263.60.04821.812650.04899.9
2.26-2.533.50.03627.311310.03699.9
2.53-2.923.50.0332.89990.0399.9
2.92-3.573.40.02542.68450.02599.9
3.57-5.053.50.02249.96560.02299.8
5.05-33.643.30.02248.23810.02299.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q9B

1q9b


Resolution: 1.602→33.355 Å / SU ML: 0.13 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 530 4.79 %RANDOM
Rwork0.1786 ---
all0.185 11140 --
obs0.1803 11067 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.602→33.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 18 85 711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006660
X-RAY DIFFRACTIONf_angle_d1.108880
X-RAY DIFFRACTIONf_dihedral_angle_d15.823242
X-RAY DIFFRACTIONf_chiral_restr0.03380
X-RAY DIFFRACTIONf_plane_restr0.004123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.602-1.76270.26961340.22282591X-RAY DIFFRACTION98
1.7627-2.01770.21061310.19362643X-RAY DIFFRACTION100
2.0177-2.5420.23631460.19022619X-RAY DIFFRACTION100
2.542-33.36220.1911190.15912684X-RAY DIFFRACTION100

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