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- PDB-5xsx: Crystal structure of an archaeal chitinase in the substrate-compl... -

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Basic information

Entry
Database: PDB / ID: 5xsx
TitleCrystal structure of an archaeal chitinase in the substrate-complex form (P212121)
ComponentsChitinase
KeywordsHYDROLASE / chitinase
Function / homology
Function and homology information


endochitinase activity / chitinase / polysaccharide binding / carbohydrate metabolic process
Similarity search - Function
Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Chitinase
Similarity search - Component
Biological speciesThermococcus chitonophagus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.642 Å
AuthorsNishitani, Y. / Miki, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
CREST Japan
CitationJournal: Glycobiology / Year: 2018
Title: Crystal structures of an archaeal chitinase ChiD and its ligand complexes.
Authors: Nishitani, Y. / Horiuchi, A. / Aslam, M. / Kanai, T. / Atomi, H. / Miki, K.
History
DepositionJun 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,69818
Polymers112,3202
Non-polymers3,37716
Water1,38777
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8479
Polymers56,1601
Non-polymers1,6878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8509
Polymers56,1601
Non-polymers1,6908
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.932, 145.196, 152.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase


Mass: 56160.203 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 321-805
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus chitonophagus (archaea) / Gene: chiD, CHITON_1119 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A161KIT4, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl (pH 8.5), NH4H2PO4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 50103 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 17.4
Reflection shellResolution: 2.65→2.71 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XSW

5xsw


Resolution: 2.642→49.626 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 2545 5.09 %
Rwork0.23 --
obs0.2315 49997 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.642→49.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 219 77 8232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028411
X-RAY DIFFRACTIONf_angle_d0.54411485
X-RAY DIFFRACTIONf_dihedral_angle_d9.9572938
X-RAY DIFFRACTIONf_chiral_restr0.0221216
X-RAY DIFFRACTIONf_plane_restr0.0031450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6417-2.69250.42191180.3562375X-RAY DIFFRACTION90
2.6925-2.74740.40091430.34352586X-RAY DIFFRACTION100
2.7474-2.80720.35261470.32192613X-RAY DIFFRACTION100
2.8072-2.87240.36041590.3092594X-RAY DIFFRACTION100
2.8724-2.94430.35681320.31652626X-RAY DIFFRACTION100
2.9443-3.02390.40071200.30432640X-RAY DIFFRACTION100
3.0239-3.11280.34381530.28882598X-RAY DIFFRACTION100
3.1128-3.21330.33041330.27922649X-RAY DIFFRACTION100
3.2133-3.32810.29671460.27862631X-RAY DIFFRACTION100
3.3281-3.46130.27341450.25032639X-RAY DIFFRACTION100
3.4613-3.61880.30821420.24612630X-RAY DIFFRACTION100
3.6188-3.80950.25551410.23532646X-RAY DIFFRACTION100
3.8095-4.04810.29181370.22192638X-RAY DIFFRACTION100
4.0481-4.36050.22021280.20032667X-RAY DIFFRACTION100
4.3605-4.7990.21341540.18552678X-RAY DIFFRACTION100
4.799-5.49270.20931450.19422681X-RAY DIFFRACTION100
5.4927-6.91720.23121340.20282738X-RAY DIFFRACTION100
6.9172-49.63520.18471680.18442823X-RAY DIFFRACTION100

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