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- PDB-6slf: Nalpha-acylglutamine aminoacylase from Corynebacterium sp.releasi... -

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Basic information

Entry
Database: PDB / ID: 6slf
TitleNalpha-acylglutamine aminoacylase from Corynebacterium sp.releasing human axilla odorants co-crystallised with high affinity inhibitor
ComponentsN-alpha-acyl-glutamine aminoacylase
KeywordsHYDROLASE / aminoacylase / inhibitor / complex / tetramer
Function / homology
Function and homology information


Nalpha-acyl-L-glutamine aminoacylase / hydrolase activity
Similarity search - Function
Amidohydrolase / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
ACETATE ION / Chem-LJ8 / N(alpha)-acyl-glutamine aminoacylase
Similarity search - Component
Biological speciesCorynebacterium striatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsNatsch, A. / Emter, R.
Citation
Journal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 2020
Title: The specific biochemistry of human axilla odour formation viewed in an evolutionary context.
Authors: Natsch, A. / Emter, R.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: A specific bacterial aminoacylase cleaves odorant precursors secreted in the human axilla.
Authors: Natsch, A. / Gfeller, H. / Gygax, P. / Schmid, J. / Acuna, G.
History
DepositionAug 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acyl-glutamine aminoacylase
B: N-alpha-acyl-glutamine aminoacylase
C: N-alpha-acyl-glutamine aminoacylase
D: N-alpha-acyl-glutamine aminoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,86024
Polymers174,1384
Non-polymers2,72320
Water18,3751020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Formation of a stable tetramer in solution in presence of the ligand AMR only was shown both with gel filtration and with native gel electophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16880 Å2
ΔGint-116 kcal/mol
Surface area51090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.688, 181.919, 93.122
Angle α, β, γ (deg.)90.000, 104.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
N-alpha-acyl-glutamine aminoacylase


Mass: 43534.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Isolate from skin in human axillae / Source: (gene. exp.) Corynebacterium striatum (bacteria) / Gene: agaA / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q8GGD4

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Non-polymers , 6 types, 1040 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-LJ8 / (2~{S})-5-azanyl-2-[[[(3~{S})-3-methyl-5-phenyl-pentyl]-oxidanyl-phosphoryl]methyl]-5-oxidanylidene-pentanoic acid


Mass: 369.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H28NO5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 90microL of 30% PEG4K, 0.22M sodium acetate, 0.1M Tris pH 8.5 + 10microL of Index screen (Hampton Research) containing 0.2M ammonium sulphate, 0.1M Bis-Tris pH6.5, 25%PEG3350

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Data collection

DiffractionMean temperature: 296 K / Ambient temp details: not exactly reported / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Sep 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.5→29.58 Å / Num. obs: 164787 / % possible obs: 100 % / Redundancy: 6.93 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.0108 / Net I/σ(I): 8.3
Reflection shellResolution: 1.5→1.8 Å / Rmerge(I) obs: 0.0418 / Num. unique obs: 164787 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.25data extraction
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XMB, 1YSJ

1xmb

1ysj


Resolution: 1.75→29.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.249 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 8738 5 %RANDOM
Rwork0.1821 ---
obs0.1835 164787 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 64.64 Å2 / Biso mean: 26.211 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.75→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12137 0 156 1020 13313
Biso mean--27.61 30.88 -
Num. residues----1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212573
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.95517109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48251581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18725.16595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.029151926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4541556
X-RAY DIFFRACTIONr_chiral_restr0.0960.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029796
X-RAY DIFFRACTIONr_nbd_refined0.2010.26480
X-RAY DIFFRACTIONr_nbtor_refined0.30.28663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.21056
X-RAY DIFFRACTIONr_metal_ion_refined0.0410.218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.215
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 673 -
Rwork0.296 12168 -
all-12841 -
obs--99.92 %

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