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- PDB-8ith: Crystal structure of lasso peptide epimerase MslH H295N -

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Basic information

Entry
Database: PDB / ID: 8ith
TitleCrystal structure of lasso peptide epimerase MslH H295N
ComponentsPoly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
KeywordsISOMERASE / epimerase / MslH / MslA / lasso peptide / RiPPs / MS-271
Function / homologyBacterial capsule synthesis protein PGA_cap / Capsule synthesis protein, CapA / Bacterial capsule synthesis protein PGA_cap / Metallo-dependent phosphatase-like / metal ion binding / Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
Function and homology information
Biological speciesStreptomyces griseorubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNakashima, Y. / Hiroyuki, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H02777 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15303 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism.
Authors: Nakashima, Y. / Kawakami, A. / Ogasawara, Y. / Maeki, M. / Tokeshi, M. / Dairi, T. / Morita, H.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.title / _citation.year
Revision 1.2Aug 23, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6125
Polymers47,2951
Non-polymers3164
Water2,054114
1
A: Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)380,89440
Polymers378,3638
Non-polymers2,53132
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area41490 Å2
ΔGint-228 kcal/mol
Surface area119000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.888, 127.888, 171.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)


Mass: 47295.359 Da / Num. of mol.: 1 / Mutation: H295N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseorubiginosus (bacteria)
Gene: EV578_104528 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V2TW40
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 200 mM magnesium chloride, 100 mM Tris-HCl, 28% (w/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.035 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 2.55→45.22 Å / Num. obs: 43288 / % possible obs: 98.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 46.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.062 / Rrim(I) all: 0.129 / Net I/σ(I): 15.1
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2797 / CC1/2: 0.787 / Rpim(I) all: 0.515 / Rrim(I) all: 1.071 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→45.22 Å / SU ML: 0.3176 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2156 3755 8.67 %
Rwork0.183 39533 -
obs0.1859 43288 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.67 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 18 114 3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223434
X-RAY DIFFRACTIONf_angle_d0.50684679
X-RAY DIFFRACTIONf_chiral_restr0.0416529
X-RAY DIFFRACTIONf_plane_restr0.0043631
X-RAY DIFFRACTIONf_dihedral_angle_d23.31281270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.580.36131450.30691471X-RAY DIFFRACTION99.32
2.58-2.620.34651320.29911505X-RAY DIFFRACTION99.27
2.62-2.650.33311340.27751499X-RAY DIFFRACTION99.09
2.65-2.690.29581420.26231454X-RAY DIFFRACTION98.82
2.69-2.730.29841320.25411479X-RAY DIFFRACTION98.65
2.73-2.770.32521470.23751482X-RAY DIFFRACTION97.78
2.77-2.820.31581360.24631438X-RAY DIFFRACTION97.16
2.82-2.870.27471370.23491446X-RAY DIFFRACTION96.29
2.87-2.920.2851370.21741444X-RAY DIFFRACTION96.76
2.92-2.980.27341440.22631460X-RAY DIFFRACTION96.57
2.98-3.040.23441390.22121434X-RAY DIFFRACTION96.86
3.04-3.10.2311390.2261447X-RAY DIFFRACTION97.36
3.1-3.170.24451270.20261489X-RAY DIFFRACTION98
3.17-3.250.24821460.19991435X-RAY DIFFRACTION98.57
3.25-3.340.21681360.18211490X-RAY DIFFRACTION97.72
3.34-3.440.22171340.17221482X-RAY DIFFRACTION97.88
3.44-3.550.19951550.16551467X-RAY DIFFRACTION98.36
3.55-3.680.19671410.15791462X-RAY DIFFRACTION98.34
3.68-3.820.16671390.15941451X-RAY DIFFRACTION98.33
3.82-40.19131600.15081468X-RAY DIFFRACTION98.13
4-4.210.15941410.14351464X-RAY DIFFRACTION98.29
4.21-4.470.16091290.13981490X-RAY DIFFRACTION98.06
4.47-4.820.18221350.14851460X-RAY DIFFRACTION97.85
4.82-5.30.18681400.1521454X-RAY DIFFRACTION97.49
5.3-6.070.22451420.1891459X-RAY DIFFRACTION97.21
6.07-7.630.21491160.19531469X-RAY DIFFRACTION96.88
7.64-45.220.19561500.17161434X-RAY DIFFRACTION95.36
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.425870420946-0.0393183543376-0.06752849195360.150986410512-0.08321967356170.1092029877670.0722436875462-0.00230972649395-0.0834673597878-0.0480605952688-0.0506684111890.0605717272153-0.193856828829-0.1384350096592.29356595533E-50.316982426661-0.00230427247593-0.005748621860310.30970832363-0.001864778187810.27379378093715.742483556717.376157695561.4287615044
20.213763582004-0.261366980595-0.1300254054670.3003904436320.07066474011430.390077163387-0.0273684996121-0.0835705486833-0.01968970355070.02912623454240.00182446568574-0.02829682540830.08169073524770.128243790541-2.41690217466E-50.261017433537-0.02230161901370.005701944417880.2889116981230.02984687950560.25855139014830.375124361518.58277343779.7047516895
30.5266864116220.205484991165-0.001783734536430.2985486603510.03829712481620.4143016351480.0460017091662-0.0552800053940.102161161722-0.0463074936702-0.0731758293061-0.0508523091368-0.035044593850.0780960123236-6.44886076991E-60.274325585583-0.01692444734560.01328967892510.3109789136040.03306604938460.31099070728729.650838461124.403391311766.5874653049
40.04934721474390.105410433993-0.03982714226510.21751499522-0.09184194593480.1641569339660.0340957044754-0.0516940677055-0.0565074156289-0.0547510101954-0.003161595767940.0126206471466-0.251917617522-0.0692393394479-1.72895000942E-60.3168886564784.10683757454E-60.03650526832950.3078700111820.05737398787260.31558039299825.254780978928.371099031848.1443592057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 201 )
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 386 )
4X-RAY DIFFRACTION4chain 'A' and (resid 387 through 439 )

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