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- PDB-5z7p: SmChiA sliding-intermediate with chitotriose -

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Basic information

Entry
Database: PDB / ID: 5z7p
TitleSmChiA sliding-intermediate with chitotriose
ComponentsChitinase AChitinase A N-terminal domain
KeywordsHYDROLASE / Chitinase / complex / intermediate
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. ...Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Chitinase A
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNakamura, A. / Iino, R.
Funding support Japan, 3items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and TechnologyJP15H06898 Japan
Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and TechnologyJP17K18429 Japan
Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and TechnologyJP17H05899 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Processive chitinase is Brownian monorail operated by fast catalysis after peeling rail from crystalline chitin.
Authors: Nakamura, A. / Okazaki, K.I. / Furuta, T. / Sakurai, M. / Iino, R.
History
DepositionJan 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1415
Polymers59,2371
Non-polymers9044
Water15,439857
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint9 kcal/mol
Surface area21280 Å2
Unit cell
Length a, b, c (Å)131.86, 199.8, 59.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Chitinase A / Chitinase A N-terminal domain


Mass: 59237.340 Da / Num. of mol.: 1 / Mutation: D313A, K369M, F396A, W539A, E540M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiA / Production host: Escherichia coli (E. coli) / References: UniProt: P07254*PLUS
#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 / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 700 mM sodium citrate, 10% methanol, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2→44.2 Å / Num. obs: 102372 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 16556 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EIB

1eib


Resolution: 2→44.2 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1884 5075 -
Rwork0.1546 --
obs-102372 99.9 %
Refinement stepCycle: LAST / Resolution: 2→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 61 857 5035

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