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- PDB-5onk: Native YndL -

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Basic information

Entry
Database: PDB / ID: 5onk
TitleNative YndL
ComponentsYndL
KeywordsHYDROLASE / PGA hydrolases
Function / homologyPoly-gamma-glutamate hydrolase / Poly-gamma-glutamate hydrolase, zinc-binding motif superfamily / Poly-gamma-glutamate hydrolase / hydrolase activity / plasma membrane / CITRATE ANION / IMIDAZOLE / Gamma-polyglutamate hydrolase PghL / UPF0714 protein YndL
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsRamaswamy, S. / Rasheed, M. / Morelli, C. / Calvio, C. / Sutton, B. / Pastore, A.
CitationJournal: 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.
History
DepositionAug 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._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: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YndL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5016
Polymers23,9861
Non-polymers5165
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-62 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 46.860, 100.070
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, 1 molecules A

#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

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Non-polymers , 5 types, 243 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1 Ammonium sulphate, 0.15 Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.6 - 2.3
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.61
22.31
ReflectionResolution: 1.03→34.2 Å / Num. obs: 76651 / % possible obs: 85 % / Redundancy: 1.9 % / Biso Wilson estimate: 11.75 Å2 / Net I/av σ(I): 2.2 / Net I/σ(I): 18.67

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A9L

3a9l


Resolution: 1.03→34.2 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.482 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18721 3847 5 %RANDOM
Rwork0.1662 ---
obs0.16726 72803 85.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.419 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.03→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 29 238 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0191712
X-RAY DIFFRACTIONr_bond_other_d0.0020.021575
X-RAY DIFFRACTIONr_angle_refined_deg2.4571.9682319
X-RAY DIFFRACTIONr_angle_other_deg1.12533630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63824.28684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13615288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1761510
X-RAY DIFFRACTIONr_chiral_restr0.2280.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021993
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02413
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_it1.3941.181837
X-RAY DIFFRACTIONr_mcbond_other1.3521.179836
X-RAY DIFFRACTIONr_mcangle_it1.9571.7781055
X-RAY DIFFRACTIONr_mcangle_other1.9561.7811056
X-RAY DIFFRACTIONr_scbond_it2.6811.475875
X-RAY DIFFRACTIONr_scbond_other2.681.476876
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9482.1251265
X-RAY DIFFRACTIONr_long_range_B_refined5.26511.6272162
X-RAY DIFFRACTIONr_long_range_B_other5.26311.6342163
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.033→1.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 63 -
Rwork0.342 959 -
obs--15.67 %

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