[English] 日本語
Yorodumi
- PDB-1k9t: Chitinase a complexed with tetra-N-acetylchitotriose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k9t
TitleChitinase a complexed with tetra-N-acetylchitotriose
ComponentsCHITINASE A
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 18 / CHITINASE / CHITINOLYSIS / A/B-(TIM)-BARREL
Function / homology
Function and homology information


chitinase activity / endochitinase activity / chitinase / 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 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II ...Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / 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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
chitinase / Chitinase A
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPrag, G. / Tucker, P.A. / Oppenheim, A.B.
Citation
Journal: To be Published
Title: Complex Structures of Chitinase A Mutant with Oligonag Provide Insight Into the Enzymatic Mechanism
Authors: Prag, G. / Tucker, P.A. / Oppenheim, A.B.
#1: Journal: Chitin Enzymol. / Year: 2001
Title: Conservation of Structural Elements and Catalytic Mechanism in the Chitinolytic Enzymes from Serratia Marcescens
Authors: Prag, G. / Vorgias, C.E. / Oppenheim, A.B.
#2: Journal: Biochemistry / Year: 2001
Title: High Resolution Structural Analyses of Mutant Chitinase a Complexes with Substrates Provide New Insight Into the Mechanism of Catalysis
Authors: Papanikolau, Y. / Prag, G. / Tavlas, G. / Vorgias, C.E. / Oppenheim, A.B. / Petratos, K.
#3: Journal: J.Am.Chem.Soc. / Year: 1997
Title: Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes
Authors: Tews, I. / Terwisscha Van Scheltinga, A.C. / Perrakis, A. / Wilson, K.S. / Dijkstra, B.W.
#4: Journal: Structure / Year: 1994
Title: Crystal Structure of a Bacterial Chitinase at 2.3 Angstrom Resolution
Authors: Perrakis, A. / Tews, I. / Dauter, Z. / Oppenheim, A.B. / Chet, I. / Wilson, K.S. / Vorgias, C.E.
History
DepositionOct 30, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / diffrn_source / 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 / pdbx_validate_close_contact / 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_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _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_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHITINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4262
Polymers58,5961
Non-polymers8311
Water13,709761
1
A: CHITINASE A
hetero molecules

A: CHITINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8534
Polymers117,1912
Non-polymers1,6622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6280 Å2
ΔGint20 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.853, 131.907, 59.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein CHITINASE A


Mass: 58595.582 Da / Num. of mol.: 1 / Mutation: D391A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Gene: CHIA / Plasmid: PKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): A9588
References: UniProt: O83008, UniProt: P07254*PLUS, 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


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE DEPOSITORS FOUND THAT RESIDUE 475 IS GLY AND THAT IT IS VARIED FROM THE SEQUENCE IN GENBANK AT ...THE DEPOSITORS FOUND THAT RESIDUE 475 IS GLY AND THAT IT IS VARIED FROM THE SEQUENCE IN GENBANK AT THIS POSITION. COMPARE ENTRIES 1EDQ, 1EHN, 1EIB, 1FFR, 1FFQ AND BAA31567(AB015996). THE CRYSTALLOGRAPHIC DATA WAS CONFIRMED BY DNA SEQUENCING. THE REASON FOR THESE DIFFERENCES IS PROBABLY DUE TO EVOLUTIONARY VARIATIONS. SEQUENCES VARIATIONS AMONG S.MARCESCENS CHITINASE A THAT WERE ISOLATED IN SEVERAL PLACES IN THE WORLD ARE KNOWN. IN THIS CASE THE STRAIN IS FROM THE COLLECTION OF PROF. ILAN CHET.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.75M CITRATE-NA AND 20%(V/V) METHANOL, pH 7.20, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 28, 2000
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 73268 / Num. obs: 73268 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.0391 / Net I/σ(I): 18.22
Reflection shellResolution: 1.8→1.85 Å / % possible all: 100

-
Processing

Software
NameClassification
XDSdata scaling
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDQ

1edq


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3687 5 %RANDOM
Rwork0.18 ---
all0.189 73268 --
obs0.189 73268 100 %-
Displacement parametersBiso mean: 23.736 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 57 761 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0230.03
X-RAY DIFFRACTIONp_planar_d0.0270.04
X-RAY DIFFRACTIONp_mcbond_it1.32
X-RAY DIFFRACTIONp_mcangle_it1.7583
X-RAY DIFFRACTIONp_scbond_it2.5623
X-RAY DIFFRACTIONp_scangle_it3.554
X-RAY DIFFRACTIONp_chiral_restr0.1160.12
X-RAY DIFFRACTIONp_singtor_nbd0.1790.5
X-RAY DIFFRACTIONp_multtor_nbd0.2550.5
X-RAY DIFFRACTIONp_planar_tor3.33
X-RAY DIFFRACTIONp_staggered_tor13.815
X-RAY DIFFRACTIONp_transverse_tor24.220

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more