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- PDB-8itg: Crystal structure of lasso peptide epimerase MslH in complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8itg
TitleCrystal structure of lasso peptide epimerase MslH in complexed with precursor peptide variant MslAW21G
Components
  • Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
  • Tricyclic peptide MS-271
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 / Tricyclic peptide MS-271 / Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
Function and homology information
Biological speciesStreptomyces griseorubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)
B: Tricyclic peptide MS-271
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9214
Polymers51,7582
Non-polymers1622
Water3,855214
1
A: Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
B: Tricyclic peptide MS-271
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)415,36532
Polymers414,06816
Non-polymers1,29816
Water28816
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 area45880 Å2
ΔGint-201 kcal/mol
Surface area115820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.232, 127.232, 170.611
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
Components on special symmetry positions
IDModelComponents
11A-828-

HOH

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Components

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


Mass: 47319.402 Da / Num. of mol.: 1
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: Protein/peptide Tricyclic peptide MS-271


Mass: 4439.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseorubiginosus (bacteria)
Gene: DWG14_02265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A385ZG42
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 214 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 200 mM magnesium chloride, 100 mM Tris-HCl (pH 9.0), 34% (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 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 2.12→45.18 Å / Num. obs: 40284 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 42.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.046 / Rrim(I) all: 0.092 / Net I/σ(I): 18.7
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3264 / CC1/2: 0.81 / Rpim(I) all: 0.466 / Rrim(I) all: 0.947 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.98 Å / SU ML: 0.1973 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 1995 5.97 %
Rwork0.1822 31446 -
obs0.1837 33441 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.76 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 8 214 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263486
X-RAY DIFFRACTIONf_angle_d0.54224753
X-RAY DIFFRACTIONf_chiral_restr0.0419534
X-RAY DIFFRACTIONf_plane_restr0.0043642
X-RAY DIFFRACTIONf_dihedral_angle_d22.98911284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.24151440.24242201X-RAY DIFFRACTION99.74
2.31-2.370.27811360.23722224X-RAY DIFFRACTION100
2.37-2.440.25771470.23692195X-RAY DIFFRACTION99.91
2.44-2.520.27041400.22592216X-RAY DIFFRACTION99.96
2.52-2.610.24141410.21642228X-RAY DIFFRACTION99.96
2.61-2.710.22531360.20552222X-RAY DIFFRACTION99.96
2.71-2.830.24451510.19262229X-RAY DIFFRACTION99.87
2.83-2.980.20881390.18232225X-RAY DIFFRACTION99.87
2.98-3.170.21551360.18272252X-RAY DIFFRACTION99.83
3.17-3.420.18571420.16822242X-RAY DIFFRACTION99.96
3.42-3.760.18751430.15752268X-RAY DIFFRACTION99.92
3.76-4.30.18111430.15282258X-RAY DIFFRACTION99.79
4.3-5.420.1691440.15932291X-RAY DIFFRACTION99.75
5.42-44.980.22751530.20582395X-RAY DIFFRACTION98.68
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)
10.894398471074-0.0806699925012-0.1358324719610.469689030766-0.2534965806090.845718322334-0.0002850872335570.0752454923888-0.0482963158902-0.0403901278104-0.06625710819390.05594988239730.00779577563889-0.0788584678328-5.94475889018E-60.298528967473-0.0002737160621190.0003013759625170.3025823617530.006034188462840.29531181304816.12700476915.219711312963.8778713114
20.255962324419-0.310242830522-0.3073534897780.4685711678190.1682429562630.5455101550880.022693788976-0.120834978614-0.06367640309510.161383479975-0.0243304724486-0.143050795890.1578342058820.237693590079-8.84389710448E-60.314284771342-0.0141792503973-0.01257684995380.4013292795130.04401663824960.31941069027333.204009131919.4902675377.5112389281
30.251515084480.1775047909970.1507427994741.59861112402-1.430717788391.79127735493-0.628439983080.0569887118695-0.132115856936-0.180179426116-0.555748159354-1.385098116580.2986823413551.08258727084-0.5734076525010.879621851111-0.01356710254060.1862754651390.8066803751840.09418793031610.79909128666342.92879963730.897668081297.4593311014
40.01880974847040.02632800708380.001519475167650.0611324909808-0.00482955991530.02207565852640.2659530896180.119838327528-0.1069956611620.387309497223-0.0166173203717-0.3706394262840.3082910077310.6121969651990.002221885590690.440881450456-0.154495085212-0.004570329695530.6567978145720.0006658186132980.52387954443644.719091542131.134326869380.2976359566
50.95518353470.6095110689710.2928896170590.428838802395-0.4484617987891.067698717930.00894582838226-0.09258112062010.216462281234-0.0115490048339-0.081384496698-0.0498196052497-0.1680125308170.05507332850172.46338695548E-60.295290526131-0.02600242041380.01203352871640.3081311554220.03508464157660.30898602502626.484471643323.100482320763.0598785204
60.4267149336870.4594351065760.04768946084810.503075443894-0.166221231470.4517499727030.02950233237960.06728075023540.253281841273-0.1052839384260.02094089154320.0572956853276-0.347700764711-0.125512853963-1.87867758961E-50.43381719518-0.0113496433860.03530689524620.4423632627030.06532392993320.38409678974225.068414763228.22540718347.9208928821
70.01864678846890.0125912746421-0.006942342605697.94497556007E-50.00402207891490.01079025061640.004287693984590.0107956173842-0.00182943876835-0.00814857866080.0351511367166-0.297402900427-0.143937443651-0.06399436018281.45350941496E-51.45987017201-0.408582534540.2790669599971.378287671810.04580274021211.3409745513826.97039194831.01589282873.5116332249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 187 )
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 211 )
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 233 )
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 386 )
6X-RAY DIFFRACTION6chain 'A' and (resid 387 through 439 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 21 )

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