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- PDB-2zxc: Ceramidase complexed with C2 -

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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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has protein modificationY
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.

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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: 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

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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

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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

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