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- PDB-4toq: Crystal structure of class III chitinase from pomegranate provide... -

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Basic information

Entry
Database: PDB / ID: 4toq
TitleCrystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity
ComponentsClass III chitinase
KeywordsHYDROLASE / chitinase / metal binding / a / b-barrel / pomegranate seed
Function / homology
Function and homology information


seedling development / amyloplast / seed germination / chitinase / chitinase activity / chitin catabolic process / polysaccharide catabolic process / calcium ion binding
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Acidic endochitinase Pun g 14, amyloplastic
Similarity search - Component
Biological speciesPunica granatum (pomegranate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMasuda, T. / Zhao, G. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2015
Title: Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity.
Authors: Masuda, T. / Zhao, G. / Mikami, B.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Nov 4, 2015Group: Data collection
Revision 1.4Jan 29, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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: Class III chitinase
B: Class III chitinase
C: Class III chitinase
D: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,62923
Polymers116,1004
Non-polymers52919
Water22,9151272
1
A: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2178
Polymers29,0251
Non-polymers1927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1806
Polymers29,0251
Non-polymers1555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1586
Polymers29,0251
Non-polymers1335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0743
Polymers29,0251
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.462, 79.969, 97.532
Angle α, β, γ (deg.)90.000, 102.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Class III chitinase


Mass: 29025.045 Da / Num. of mol.: 4 / Fragment: UNP residues 27-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Punica granatum (pomegranate) / Gene: PSC / Production host: Escherichia coli (E. coli) / References: UniProt: G1UH28, chitinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1272 / 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: 1.91 Å3/Da / Density % sol: 35.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG3350, Tris-HCl, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 111603 / % possible obs: 96.5 % / Redundancy: 5 % / Biso Wilson estimate: 13.13 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.939 / Net I/av σ(I): 30.725 / Net I/σ(I): 12.1 / Num. measured all: 558123
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.664.60.412107081.7693.4
1.66-1.724.70.335108221.77593.7
1.72-1.84.70.262108831.79294.6
1.8-1.94.80.194108711.83194.5
1.9-2.024.90.136110261.85695.7
2.02-2.175.10.1112551.84497.3
2.17-2.395.20.077113481.78698.5
2.39-2.745.30.061114611.69398.9
2.74-3.455.40.046115421.85299.3
3.45-505.20.049116873.06299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data processing
MOLREPphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOLREPmodel building
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30.595 Å / FOM work R set: 0.8777 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 5612 5.03 %
Rwork0.1547 105932 -
obs0.1566 111544 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.57 Å2 / Biso mean: 14.7 Å2 / Biso min: 4.18 Å2
Refinement stepCycle: final / Resolution: 1.6→30.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8159 0 19 1272 9450
Biso mean--22.24 23.38 -
Num. residues----1089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018741
X-RAY DIFFRACTIONf_angle_d1.14612039
X-RAY DIFFRACTIONf_chiral_restr0.0841342
X-RAY DIFFRACTIONf_plane_restr0.0051573
X-RAY DIFFRACTIONf_dihedral_angle_d12.3533093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5982-1.61630.2351790.19683323350292
1.6163-1.63540.28031730.19093407358094
1.6354-1.65530.22061630.18633397356093
1.6553-1.67630.23131950.17793389358493
1.6763-1.69830.22931620.17993454361694
1.6983-1.72160.23731650.17633456362193
1.7216-1.74620.22051890.17553414360395
1.7462-1.77220.22321700.17593473364393
1.7722-1.79990.23082130.17013428364196
1.7999-1.82940.23031720.1753441361394
1.8294-1.8610.23011850.16343476366196
1.861-1.89480.21161760.16283418359494
1.8948-1.93120.23691980.15973497369596
1.9312-1.97070.18651640.15513503366795
1.9707-2.01350.19462100.16323454366495
2.0135-2.06030.20782050.16073550375597
2.0603-2.11180.21261880.1513568375697
2.1118-2.16890.18961760.14693563373997
2.1689-2.23270.1862060.14633589379599
2.2327-2.30480.17451900.15643599378998
2.3048-2.38710.22292040.15643571377599
2.3871-2.48260.19161810.16253672385399
2.4826-2.59560.22021970.16663594379199
2.5956-2.73230.20981920.17513627381999
2.7323-2.90340.20051810.17293655383699
2.9034-3.12740.20491850.163655384099
3.1274-3.44170.15842090.13983652386199
3.4417-3.93890.13662000.125636673867100
3.9389-4.95910.1431870.120636903877100
4.9591-30.60080.17511970.15083750394799

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