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- PDB-6b8c: Crystal structure of NlpC/p60 domain of peptidoglycan hydrolase SagA -

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Basic information

Entry
Database: PDB / ID: 6b8c
TitleCrystal structure of NlpC/p60 domain of peptidoglycan hydrolase SagA
ComponentsNLP/P60
KeywordsHYDROLASE / peptidoglycan endopeptidase
Function / homology:
Function and homology information
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsKim, B. / Oren, D.A. / Hang, H.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1 TR0018663 United States
CitationJournal: Elife / Year: 2019
Title: Enterococcus faeciumsecreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis.
Authors: Kim, B. / Wang, Y.C. / Hespen, C.W. / Espinosa, J. / Salje, J. / Rangan, K.J. / Oren, D.A. / Kang, J.Y. / Pedicord, V.A. / Hang, H.C.
History
DepositionOct 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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: NLP/P60


Theoretical massNumber of molelcules
Total (without water)15,7151
Polymers15,7151
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, gel filtration, Based on size-exclusion chromatography, it seems it is a monomer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NLP/P60
x 8


Theoretical massNumber of molelcules
Total (without water)125,7228
Polymers125,7228
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_758-x+2,y,-z+31
crystal symmetry operation4_578x,-y+2,-z+31
crystal symmetry operation13_558y,x,-z+31
crystal symmetry operation14_778-y+2,-x+2,-z+31
crystal symmetry operation15_575y,-x+2,z1
crystal symmetry operation16_755-y+2,x,z1
Buried area11030 Å2
ΔGint-82 kcal/mol
Surface area35180 Å2
MethodPISA
3
A: NLP/P60

A: NLP/P60


Theoretical massNumber of molelcules
Total (without water)31,4302
Polymers31,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_758-x+2,y,-z+31
Buried area1280 Å2
ΔGint-9 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.385, 100.385, 100.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

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Components

#1: Protein NLP/P60 / SagA


Mass: 15715.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: FM130_01170 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A1T4J4N4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2 M ammonium sulfate, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 8107 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / CC1/2: 0.997 / Rpim(I) all: 0.035 / Rsym value: 0.109 / Χ2: 1.79 / Net I/σ(I): 38.5
Reflection shellΧ2: 0.55

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDY

4fdy


Resolution: 2.403→44.894 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 717 10.02 %
Rwork0.2395 --
obs0.2426 7155 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.403→44.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 0 8 878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003898
X-RAY DIFFRACTIONf_angle_d0.641225
X-RAY DIFFRACTIONf_dihedral_angle_d16.418496
X-RAY DIFFRACTIONf_chiral_restr0.049126
X-RAY DIFFRACTIONf_plane_restr0.005158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4031-2.58860.43561350.44471200X-RAY DIFFRACTION96
2.5886-2.84910.25771380.28871254X-RAY DIFFRACTION100
2.8491-3.26130.34921420.27831274X-RAY DIFFRACTION100
3.2613-4.10840.241440.21981292X-RAY DIFFRACTION100
4.1084-44.90140.25271580.21711418X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 108.8705 Å / Origin y: 79.4809 Å / Origin z: 140.5608 Å
111213212223313233
T0.8184 Å20.1049 Å20.3078 Å2-0.5217 Å20.0023 Å2--0.6144 Å2
L3.3137 °2-0.3359 °2-0.1809 °2-4.0585 °2-0.2465 °2--3.0088 °2
S-0.5963 Å °0.2273 Å °-0.7064 Å °-0.256 Å °-0.027 Å °-0.2792 Å °1.0093 Å °0.3578 Å °0.4618 Å °
Refinement TLS groupSelection details: all

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