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- PDB-2cjl: CRYSTAL STRUCTURE AND ENZYMATIC PROPERTIES OF A BACTERIAL FAMILY ... -

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Basic information

Entry
Database: PDB / ID: 2cjl
TitleCRYSTAL STRUCTURE AND ENZYMATIC PROPERTIES OF A BACTERIAL FAMILY 19 CHITINASE REVEAL DIFFERENCES WITH PLANT ENZYMES
ComponentsSECRETED CHITINASE
KeywordsHYDROLASE / PLANT ENZYMES
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / cell wall macromolecule catabolic process / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle ...Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHoell, I.A. / Dalhus, B. / Heggset, E.B. / Aspmo, S.I. / Eijsink, V.G.H.
CitationJournal: FEBS J. / Year: 2006
Title: Crystal Structure and Enzymatic Properties of a Bacterial Family 19 Chitinase Reveal Differences with Plant Enzymes
Authors: Hoell, I.A. / Dalhus, B. / Heggset, E.B. / Aspmo, S.I. / Eijsink, V.G.H.
History
DepositionApr 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SECRETED CHITINASE
B: SECRETED CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2206
Polymers43,9582
Non-polymers2624
Water5,585310
1
A: SECRETED CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1103
Polymers21,9791
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SECRETED CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1103
Polymers21,9791
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.671, 74.378, 64.179
Angle α, β, γ (deg.)90.00, 108.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SECRETED CHITINASE / CHITINASE G


Mass: 21978.957 Da / Num. of mol.: 2 / Fragment: RESIDUES 41-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: A3 (2) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8CK55, chitinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.82 Å3/Da / Density % sol: 56.38 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.5→74.33 Å / Num. obs: 64934 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WVV

1wvv


Resolution: 1.5→74.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.187 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3437 5 %RANDOM
Rwork0.187 ---
obs0.188 64934 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20.22 Å2
2---0.44 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 4 310 3414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9284352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.785406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01825.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05615436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5051510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21557
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22250
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.52046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1723202
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.83831325
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6854.51150
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 238
Rwork0.244 4738

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