[English] 日本語
Yorodumi
- PDB-3fxy: Acidic Mammalian Chinase, Catalytic Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fxy
TitleAcidic Mammalian Chinase, Catalytic Domain
ComponentsAcidic mammalian chitinase
KeywordsHYDROLASE / CHITINASE / ASTHMA / CHITIN DEGRADATION / 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 activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / immune system process ...chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / immune system process / 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 ...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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
Acidic mammalian chitinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acidic mammalian chitinase
B: Acidic mammalian chitinase
C: Acidic mammalian chitinase
D: Acidic mammalian chitinase


Theoretical massNumber of molelcules
Total (without water)176,8134
Polymers176,8134
Non-polymers00
Water8,953497
1
A: Acidic mammalian chitinase


Theoretical massNumber of molelcules
Total (without water)44,2031
Polymers44,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acidic mammalian chitinase


Theoretical massNumber of molelcules
Total (without water)44,2031
Polymers44,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acidic mammalian chitinase


Theoretical massNumber of molelcules
Total (without water)44,2031
Polymers44,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Acidic mammalian chitinase


Theoretical massNumber of molelcules
Total (without water)44,2031
Polymers44,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.941, 92.360, 111.669
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Acidic mammalian chitinase / AMCase / TSA1902


Mass: 44203.371 Da / Num. of mol.: 4 / Fragment: UNP residues 22-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIA / Production host: Chinese Hamster (Chinese hamster) / References: UniProt: Q9BZP6, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 3350, 120 mM ammonium sulfate, 60 mM sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
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: 2→50 Å / Num. all: 93507 / Num. obs: 91479 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.77

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.15 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.228 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22838 4695 5 %RANDOM
Rwork0.1971 ---
all0.19868 90602 --
obs0.19868 88718 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.36 Å2
2---0.65 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11947 0 0 497 12444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02212332
X-RAY DIFFRACTIONr_angle_refined_deg1.061.93116823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19351505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61224.932590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.996151848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.411528
X-RAY DIFFRACTIONr_chiral_restr0.0750.21737
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029704
X-RAY DIFFRACTIONr_nbd_refined0.1790.25697
X-RAY DIFFRACTIONr_nbtor_refined0.3020.28428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2652
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.2157
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.240
X-RAY DIFFRACTIONr_mcbond_it0.3781.57736
X-RAY DIFFRACTIONr_mcangle_it0.61212059
X-RAY DIFFRACTIONr_scbond_it0.93935510
X-RAY DIFFRACTIONr_scangle_it1.4384.54764
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 316 -
Rwork0.247 6015 -
obs--90.68 %

+
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