[English] 日本語
Yorodumi
- PDB-2zxc: Ceramidase complexed with C2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zxc
TitleCeramidase complexed with C2
ComponentsNeutral ceramidase
KeywordsHYDROLASE / BETA-PRISM FOLD SURROUNDED BY SIX ALPHA HELIX / Lipid metabolism / Secreted
Function / homology
Function and homology information


sphingosine catabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / sphingosine biosynthetic process / long-chain fatty acid biosynthetic process / extracellular region / metal ion binding
Similarity search - Function
Neutral/alkaline non-lysosomal ceramidase, C-terminal domain / Neutral/alkaline nonlysosomal ceramidase / Neutral/alkaline non-lysosomal ceramidase, N-terminal / Neutral/alkaline non-lysosomal ceramidase, C-terminal / Neutral ceramidase, C-terminal domain superfamily / Neutral/alkaline non-lysosomal ceramidase, N-terminal / Neutral/alkaline non-lysosomal ceramidase, C-terminal / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-2ED / FORMIC ACID / Neutral ceramidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOkano, H. / Inoue, T. / Okino, N. / Kakuta, Y. / Matsumura, H. / Ito, M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase.
Authors: Inoue, T. / Okino, N. / Kakuta, Y. / Hijikata, A. / Okano, H. / Goda, H.M. / Tani, M. / Sueyoshi, N. / Kambayashi, K. / Matsumura, H. / Kai, Y. / Ito, M.
History
DepositionDec 22, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutral ceramidase
B: Neutral ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,09718
Polymers141,7112
Non-polymers1,38716
Water16,916939
1
A: Neutral ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4718
Polymers70,8551
Non-polymers6157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutral ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,62710
Polymers70,8551
Non-polymers7729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.741, 65.800, 340.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Neutral ceramidase / NCDase / Acylsphingosine deacylase / N-acylsphingosine amidohydrolase


Mass: 70855.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I596, ceramidase

-
Non-polymers , 6 types, 955 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-2ED / N-[(1R,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]acetamide / C2-ceramide


Mass: 341.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H39NO3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsABOUT THE CONFLICTS OF RESIDUE 157, 172 AND 574, REFERE TO UNP Q9I596 REFERENCE 1 AND THE GENBANK ...ABOUT THE CONFLICTS OF RESIDUE 157, 172 AND 574, REFERE TO UNP Q9I596 REFERENCE 1 AND THE GENBANK DATABASE BAA88409.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 14% PEG3350, 200mM Ammonium Formate, 1mM C2-seramide, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 103094 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 6.1
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.42 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native structure

Resolution: 2.2→35.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 51380.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3739 5.1 %RANDOM
Rwork0.194 ---
obs0.194 73838 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.8714 Å2 / ksol: 0.317328 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.59 Å20 Å20 Å2
2---0.46 Å20 Å2
3----7.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9942 0 62 939 10943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d2.3
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 650 5.4 %
Rwork0.225 11424 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4c26.paramc26.top
X-RAY DIFFRACTION5ligand.paramligand.top

+
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://pdbjlvh1.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