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- PDB-4cyy: The structure of vanin-1: defining the link between metabolic dis... -

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Basic information

Entry
Database: PDB / ID: 4cyy
TitleThe structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
ComponentsPANTETHEINASE
KeywordsHYDROLASE / INFLAMMATION / OXIDATIVE STRESS / METABOLIC DISEASE / COA BIOSYNTHESIS
Function / homology
Function and homology information


pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / positive regulation of T cell differentiation in thymus / Post-translational modification: synthesis of GPI-anchored proteins / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / positive regulation of T cell differentiation in thymus / Post-translational modification: synthesis of GPI-anchored proteins / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / azurophil granule membrane / side of membrane / cell-cell adhesion / response to oxidative stress / inflammatory response / innate immune response / Neutrophil degranulation / extracellular region / membrane / plasma membrane
Similarity search - Function
Biotinidase-like, eukaryotic / Biotinidase/VNN family / Vanin, C-terminal / Vanin C-terminal domain / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase ...Biotinidase-like, eukaryotic / Biotinidase/VNN family / Vanin, C-terminal / Vanin C-terminal domain / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsBoersma, Y.L. / Newman, J. / Adams, T.E. / Sparrow, L. / Cowieson, N. / Lucent, D. / Krippner, G. / Bozaoglu, K. / Peat, T.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Structure of Vanin-1: A Key Enzyme Linking Metabolic Disease and Inflammation
Authors: Boersma, Y.L. / Newman, J. / Adams, T.E. / Cowieson, N. / Krippner, G. / Bozaoglu, K. / Peat, T.S.
History
DepositionApr 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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
Revision 2.2Nov 20, 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: PANTETHEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6346
Polymers56,3251
Non-polymers1,3095
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.904, 101.904, 133.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PANTETHEINASE / PANTETHEINE HYDROLASE / TIFF66 / VASCULAR NON-INFLAMMATORY MOLECULE 1 / VANIN-1


Mass: 56325.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FLAG-TAG AT THE N-TERMINUS AND PRO-PEPTIDE AT THE C-TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE FORM OF THE PROTEIN.
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O95497, pantetheine hydrolase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFLAG TAG AT N-TERMINUS AND THE PRO-PEPTIDE AT THE C- TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE ...FLAG TAG AT N-TERMINUS AND THE PRO-PEPTIDE AT THE C- TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE FORM OF THE PROTEIN. IN ADDITION THE DEPOSITED STRUCTURE HAS THE NATURALLY OCCURRING THR26ILE SNP IN THE SEQUENCE.

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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: 3.91 Å3/Da / Density % sol: 68.6 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: THE PROTEIN WAS AT 15 MG/ML. THE RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE SET UP AT 8 C AND THE DROPS WERE ...Details: THE PROTEIN WAS AT 15 MG/ML. THE RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE SET UP AT 8 C AND THE DROPS WERE 150 NL PLUS 150 NL IN SITTING DROP PLATES.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.89→47.6 Å / Num. obs: 18526 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 16.3 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 14.5
Reflection shellResolution: 2.89→3.04 Å / Redundancy: 16.1 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.7 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CYF

4cyf


Resolution: 2.89→88.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.219 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.6 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21883 947 5.1 %RANDOM
Rwork0.17425 ---
obs0.17646 17545 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.539 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å21.42 Å20 Å2
2--2.84 Å20 Å2
3----9.23 Å2
Refinement stepCycle: LAST / Resolution: 2.89→88.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 84 11 3710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193803
X-RAY DIFFRACTIONr_bond_other_d0.0010.023459
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.975184
X-RAY DIFFRACTIONr_angle_other_deg0.7137953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0315459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19824.682173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28815583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3721513
X-RAY DIFFRACTIONr_chiral_restr0.0640.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02876
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6775.8441842
X-RAY DIFFRACTIONr_mcbond_other2.6755.8431841
X-RAY DIFFRACTIONr_mcangle_it4.3098.762299
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8166.5271961
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.887→2.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 80 -
Rwork0.31 1226 -
obs--95.75 %

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