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- PDB-5onl: YNDL-apo (Zinc-free) -

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Basic information

Entry
Database: PDB / ID: 5onl
TitleYNDL-apo (Zinc-free)
ComponentsYndL
KeywordsHYDROLASE / Gamma-PGA-hydrolases
Function / homology
Function and homology information


hydrolase activity / plasma membrane
Similarity search - Function
Poly-gamma-glutamate hydrolase / Poly-gamma-glutamate hydrolase, zinc-binding motif superfamily / Poly-gamma-glutamate hydrolase
Similarity search - Domain/homology
phenylmethanol / fluoroacetic acid / CITRATE ANION / Gamma-polyglutamate hydrolase PghL / UPF0714 protein YndL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Mar 4, 2020Group: Database references / Category: citation / citation_author
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 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: YndL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0075
Polymers23,5351
Non-polymers4714
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-15 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.612, 47.284, 99.893
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: 23535.217 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, 206 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-010 / phenylmethanol


Mass: 108.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O
#4: Chemical ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3FO2
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.86 Å3/Da / Density % sol: 33.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 1 Ammonium Sulphate, 0.15 M Sodium Citrate

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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: 20566 / % possible obs: 99 % / Redundancy: 1.9 % / Biso Wilson estimate: 17.25 Å2 / Net I/σ(I): 22.75

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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: 1.7→15.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.463 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21218 1056 5.1 %RANDOM
Rwork0.17364 ---
obs0.17563 19450 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.129 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→15.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 31 202 1814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191699
X-RAY DIFFRACTIONr_bond_other_d0.0030.021571
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.9692297
X-RAY DIFFRACTIONr_angle_other_deg1.06333623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58524.19881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17315288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5171510
X-RAY DIFFRACTIONr_chiral_restr0.1970.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021977
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02405
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_it1.8091.633840
X-RAY DIFFRACTIONr_mcbond_other1.7781.623836
X-RAY DIFFRACTIONr_mcangle_it2.6492.4321055
X-RAY DIFFRACTIONr_mcangle_other2.6472.4391056
X-RAY DIFFRACTIONr_scbond_it3.1462.015859
X-RAY DIFFRACTIONr_scbond_other2.9842.009857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6182.9161242
X-RAY DIFFRACTIONr_long_range_B_refined6.75415.2172105
X-RAY DIFFRACTIONr_long_range_B_other6.73515.1432101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 78 -
Rwork0.256 1366 -
obs--95.95 %

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