[English] 日本語
Yorodumi
- PDB-3fy1: The Acidic Mammalian Chitinase catalytic domain in complex with m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fy1
TitleThe Acidic Mammalian Chitinase catalytic domain in complex with methylallosamidin
ComponentsAcidic mammalian chitinase
KeywordsHYDROLASE / CHITINASE / ASTHMA / INHIBITOR / CHITIN DEGRADATION / METHYLALLOSAMIDIN / Alternative splicing / Carbohydrate metabolism / Chitin-binding / Cytoplasm / Glycosidase / Polymorphism / Polysaccharide degradation / Secreted
Function / homology
Function and homology information


chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / immune system process / chitin binding / polysaccharide catabolic process ...chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / immune system process / chitin binding / polysaccharide catabolic process / positive regulation of chemokine production / kinase binding / apoptotic process / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / 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 ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / 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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ALLOSAMIZOLINE / Acidic mammalian chitinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOlland, A.M.
CitationJournal: Protein Sci. / Year: 2009
Title: Triad of polar residues implicated in pH specificity of acidic mammalian chitinase.
Authors: Olland, A.M. / Strand, J. / Presman, E. / Czerwinski, R. / Joseph-McCarthy, D. / Krykbaev, R. / Schlingmann, G. / Chopra, R. / Lin, L. / Fleming, M. / Kriz, R. / Stahl, M. / Somers, W. / Fitz, L. / Mosyak, L.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acidic mammalian chitinase
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7166
Polymers88,4072
Non-polymers1,3094
Water10,485582
1
A: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8583
Polymers44,2031
Non-polymers6552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acidic mammalian chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8583
Polymers44,2031
Non-polymers6552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.688, 89.287, 126.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Acidic mammalian chitinase / AMCase / TSA1902


Mass: 44203.371 Da / Num. of mol.: 2 / Fragment: UNP residues 22-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIA / Plasmid: pTMED / Production host: Chinese Hamster (Chinese hamster) / References: UniProt: Q9BZP6, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-6-O-methyl-alpha-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose


Type: oligosaccharide / Mass: 438.427 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2222h-1b_1-5_2*NCC/3=O][a2222h-1a_1-5_2*NCC/3=O_6*OC]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-AllpNAc]{[(4+1)][b-D-AllpNAc6Me]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-AMI / ALLOSAMIZOLINE


Mass: 216.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS THESE POSITIONS ARE LABELED AS SNPS. THIS WAS THE SEQUENCE THE AUTHORS GOT ...ACCORDING TO THE AUTHORS THESE POSITIONS ARE LABELED AS SNPS. THIS WAS THE SEQUENCE THE AUTHORS GOT IN ALL CLONES WHEN THEY CLONED AMCASE, AND SINCE SNP FREQUENCY WAS NOT INDICATED IN THE GENOMIC DATABASE, THEY KEPT THIS CLONE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 200 mM ammonium formate, 1 mM methylallosamidin, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2004
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 77763 / Num. obs: 71824 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.21
Reflection shellResolution: 1.7→1.744 Å / Num. unique all: 4988 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1GUV

1guv


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.898 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19391 3586 5 %RANDOM
Rwork0.17479 ---
all0.17573 76141 --
obs0.17573 68238 89.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.473 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 88 582 6620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226237
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9488518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2985752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25824.898294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33215927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4031514
X-RAY DIFFRACTIONr_chiral_restr0.1790.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024850
X-RAY DIFFRACTIONr_nbd_refined0.1850.23187
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.080.2554
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.223
X-RAY DIFFRACTIONr_mcbond_it0.5711.53830
X-RAY DIFFRACTIONr_mcangle_it0.75725996
X-RAY DIFFRACTIONr_scbond_it1.26332849
X-RAY DIFFRACTIONr_scangle_it1.7674.52520
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 269 -
Rwork0.284 4988 -
obs--89.5 %

+
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