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

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Basic information

Entry
Database: PDB / ID: 5xsw
TitleCrystal structure of an archaeal chitinase in the substrate-complex form (P63)
ComponentsChitinase
KeywordsHYDROLASE / chitinase
Function / homology
Function and homology information


chitinase / chitinase activity / 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 / SIR / Resolution: 1.95 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 / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,65420
Polymers112,3202
Non-polymers2,33418
Water16,177898
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-32 kcal/mol
Surface area37330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.253, 182.253, 110.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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

Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl (pH 8.5), NH4H2PO4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 151396 / % possible obs: 99.5 % / Redundancy: 10.2 % / Net I/σ(I): 24.5
Reflection shellResolution: 1.95→2.02 Å

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Processing

Software
NameVersionClassification
HKL-2000data processing
SOLVEphasing
RESOLVEphasing
Cootmodel building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SIR / Resolution: 1.95→47.525 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.41
RfactorNum. reflection% reflection
Rfree0.1962 7613 5.03 %
Rwork0.1665 --
obs0.168 151366 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 150 898 8984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0198427
X-RAY DIFFRACTIONf_angle_d1.53811502
X-RAY DIFFRACTIONf_dihedral_angle_d12.9142982
X-RAY DIFFRACTIONf_chiral_restr0.0981199
X-RAY DIFFRACTIONf_plane_restr0.0091463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9495-1.97160.28632540.2734735X-RAY DIFFRACTION99
1.9716-1.99480.29232780.25564761X-RAY DIFFRACTION99
1.9948-2.01910.26472450.23864732X-RAY DIFFRACTION99
2.0191-2.04470.25992570.22474753X-RAY DIFFRACTION99
2.0447-2.07160.26782500.22234813X-RAY DIFFRACTION99
2.0716-2.10.25552610.21984676X-RAY DIFFRACTION98
2.1-2.130.24982630.21434798X-RAY DIFFRACTION99
2.13-2.16180.26592610.20014756X-RAY DIFFRACTION100
2.1618-2.19550.21532480.19164752X-RAY DIFFRACTION99
2.1955-2.23150.26892510.19314775X-RAY DIFFRACTION99
2.2315-2.270.21942390.18824818X-RAY DIFFRACTION99
2.27-2.31130.21632370.18674790X-RAY DIFFRACTION100
2.3113-2.35570.22682470.17984792X-RAY DIFFRACTION100
2.3557-2.40380.20682420.17934770X-RAY DIFFRACTION100
2.4038-2.45610.20772580.17264833X-RAY DIFFRACTION100
2.4561-2.51320.20882330.17484806X-RAY DIFFRACTION100
2.5132-2.57610.23662320.18034791X-RAY DIFFRACTION99
2.5761-2.64570.22552510.17784761X-RAY DIFFRACTION100
2.6457-2.72360.18632560.16934813X-RAY DIFFRACTION100
2.7236-2.81150.22172500.1724820X-RAY DIFFRACTION100
2.8115-2.91190.19762550.16844801X-RAY DIFFRACTION100
2.9119-3.02850.19382370.17264808X-RAY DIFFRACTION100
3.0285-3.16630.20872570.16664827X-RAY DIFFRACTION100
3.1663-3.33320.17992590.16634770X-RAY DIFFRACTION99
3.3332-3.5420.19622650.15754814X-RAY DIFFRACTION100
3.542-3.81540.20062780.15164813X-RAY DIFFRACTION100
3.8154-4.19910.15052530.13394828X-RAY DIFFRACTION100
4.1991-4.80620.14872460.12444871X-RAY DIFFRACTION100
4.8062-6.05340.16532700.14284792X-RAY DIFFRACTION99
6.0534-47.53960.17222800.16934884X-RAY DIFFRACTION99

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