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- PDB-5onj: YnDL in Complex with 5 amino acid (PGA) complex -

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Basic information

Entry
Database: PDB / ID: 5onj
TitleYnDL in Complex with 5 amino acid (PGA) complex
Components
  • (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL
  • YndL
KeywordsHYDROLASE / PGA-HYDROLASE
Function / homologyPoly-gamma-glutamate hydrolase / Poly-gamma-glutamate hydrolase, zinc-binding motif superfamily / Poly-gamma-glutamate hydrolase / hydrolase activity / plasma membrane / Gamma-polyglutamate hydrolase PghL / UPF0714 protein YndL
Function and homology information
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRamaswamy, S. / Rasheed, M. / Morelli, C. / Calvio, C. / Sutton, B. / Pastore, A.
Citation
Journal: Febs J. / Year: 2018
Title: The structure of PghL hydrolase bound to its substrate poly-gamma-glutamate.
Authors: Ramaswamy, S. / Rasheed, M. / Morelli, C.F. / Calvio, C. / Sutton, B.J. / Pastore, A.
#1: Journal: To Be Published
Title: Poly-gamma-glutamate hydrolases structure: a potential strategy against Staphylococcus infectivity
Authors: Ramaswamy, S. / Rasheed, M. / Morelli, C. / Calvio, C. / Sutton, B. / Pastore, A.
History
DepositionAug 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
Revision 1.3Jan 17, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YndL
D: (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8443
Polymers24,7782
Non-polymers651
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-39 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.592, 47.651, 99.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein YndL


Mass: 23985.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_0239 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164XNU3, UniProt: O31815*PLUS
#2: Protein/peptide (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL


Mass: 792.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.86 Å3/Da / Density % sol: 33.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1M Sodium Acetate, 5% gamma-PGA, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→15.75 Å / Num. obs: 20613 / % possible obs: 99 % / Redundancy: 1.9 % / Biso Wilson estimate: 14.34 Å2 / Net I/σ(I): 24.58

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A9L

3a9l


Resolution: 1.7→15.75 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.28
RfactorNum. reflection% reflection
Rfree0.2035 1087 5.27 %
Rwork0.167 --
obs0.169 20609 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→15.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 56 228 1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061709
X-RAY DIFFRACTIONf_angle_d0.7842311
X-RAY DIFFRACTIONf_dihedral_angle_d16.4161029
X-RAY DIFFRACTIONf_chiral_restr0.06248
X-RAY DIFFRACTIONf_plane_restr0.005310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77730.24521120.18152322X-RAY DIFFRACTION96
1.7773-1.87090.23551420.18552354X-RAY DIFFRACTION98
1.8709-1.9880.26371410.18572399X-RAY DIFFRACTION99
1.988-2.14120.18711390.16472429X-RAY DIFFRACTION100
2.1412-2.35620.19781350.16912445X-RAY DIFFRACTION100
2.3562-2.69610.20131330.16562471X-RAY DIFFRACTION100
2.6961-3.39250.21061450.17232494X-RAY DIFFRACTION100
3.3925-17.29040.17581400.15242608X-RAY DIFFRACTION100

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