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- PDB-4w5z: High resolution crystal structure of catalytic domain of Chitinas... -

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Basic information

Entry
Database: PDB / ID: 4w5z
TitleHigh resolution crystal structure of catalytic domain of Chitinase 60 from psychrophilic bacteria Moritella marina.
ComponentsChitinase 60
KeywordsHYDROLASE / Tim barrel / catalytic domain / high resolution / psychrophilic chitinase
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 ...Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chitinase 60
Similarity search - Component
Biological speciesVibrio marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å
AuthorsMalecki, P.H. / Vorgias, C.E. / Rypniewski, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
The project was co-funded by the European Union within the European Regional Development Fund. Poland
CitationJournal: To Be Published
Title: High resolution crystal structure of catalytic domain of Chitinase 60 from psychrophilic bacteria Moritella marina.
Authors: Malecki, P.H. / Vorgias, C.E. / Rypniewski, W.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,89615
Polymers38,3461
Non-polymers55014
Water6,738374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-81 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.691, 72.686, 171.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-405-

NA

21A-549-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chitinase 60


Mass: 38345.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Signal peptide has been processed by E. coli. / Source: (gene. exp.) Vibrio marinus (bacteria) / Gene: chi60 / Production host: Escherichia coli (E. coli) / References: UniProt: B1VBB0, chitinase

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Non-polymers , 5 types, 388 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 45% v/v MPD, 0.2M ammonium acetate and 0.1M Bis Tris pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.976265 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 11, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976265 Å / Relative weight: 1
ReflectionNumber: 405015 / Rmerge(I) obs: 0.054 / Χ2: 1.12 / D res high: 1.32 Å / Num. obs: 74674 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
3.9485.585297510.023
2.793.94517110.028
2.282.79666910.039
1.972.28784510.056
1.761.97881810.096
1.611.76978410.184
1.491.611051810.337
1.41.491134310.607
1.321.41155111.043
ReflectionResolution: 1.32→85.585 Å / Num. all: 74674 / Num. obs: 74674 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.42 % / Biso Wilson estimate: 16.08 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.059 / Χ2: 1.124 / Net I/σ(I): 17.06 / Num. measured all: 405015
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.32-1.45.320.5571.0431.716140412063115511.15995.8
1.4-1.490.8020.60736145411363113430.67499.8
1.49-1.610.9320.3375.375622410533105180.37499.9
1.61-1.760.980.1849.3454316979097840.20399.9
1.76-1.970.9940.09616.8549689883188180.10699.9
1.97-2.280.9970.05628.1643608785478450.06299.9
2.28-2.790.9980.03938.9936348668166690.04399.8
2.79-3.940.9990.02851.6627005521451710.03199.2
3.940.9990.02359.0114967300229750.02599.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.44 Å85.58 Å
Translation1.44 Å85.58 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1772)refinement
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MB3

4mb3


Resolution: 1.32→85.585 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1501 1121 1.5 %Random selection
Rwork0.1107 73553 --
obs0.1113 74674 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.17 Å2 / Biso mean: 22.0961 Å2 / Biso min: 9.94 Å2
Refinement stepCycle: final / Resolution: 1.32→85.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 53 389 2993
Biso mean--32.33 37.48 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212733
X-RAY DIFFRACTIONf_angle_d1.8173741
X-RAY DIFFRACTIONf_chiral_restr0.123396
X-RAY DIFFRACTIONf_plane_restr0.011504
X-RAY DIFFRACTIONf_dihedral_angle_d13.608985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3155-1.37540.35081330.28678680881395
1.3754-1.44790.20951390.17791659304100
1.4479-1.53860.19261400.121691949334100
1.5386-1.65750.18111400.104991549294100
1.6575-1.82430.15631400.088592419381100
1.8243-2.08830.13111410.085192449385100
2.0883-2.6310.11441420.105393389480100
2.631-85.76620.1471460.10939537968399

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