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

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Basic information

Entry
Database: PDB / ID: 8gqa
TitleCrystal structure of lasso peptide epimerase MslH in complexed with precursor peptide analog MslAdeltaW21
Components
  • Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
  • precursor peptide analog MslAdeltaW21
KeywordsISOMERASE / epimerase / MslH
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 sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsNakashima, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02777 Japan
Japan Society for the Promotion of Science (JSPS)22K15303 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
DepositionAug 29, 2022Deposition 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
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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: precursor peptide analog MslAdeltaW21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4814
Polymers49,3192
Non-polymers1622
Water3,729207
1
A: Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
B: precursor peptide analog MslAdeltaW21
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)395,84832
Polymers394,55016
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 area48850 Å2
ΔGint-167 kcal/mol
Surface area115320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.033, 128.033, 171.026
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-795-

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
Details: WP_063802928.1 / Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: EV578_104528 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V2TW40
#2: Protein/peptide precursor peptide analog MslAdeltaW21


Mass: 1999.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B2H412
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 5.00 mg/mL MslH, 1.89 mg/mL MslAdeltaW21 with MslB1, 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: 1.045 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.29→45.27 Å / Num. obs: 61142 / % possible obs: 100 % / Redundancy: 27.7 % / Biso Wilson estimate: 43.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Net I/σ(I): 19
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 28.9 % / Rmerge(I) obs: 1.76 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3336 / CC1/2: 0.867 / % 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
Starting model: 8GQ9

8gq9


Resolution: 2.29→45.27 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.3367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 2891 4.73 %
Rwork0.1844 58251 -
obs0.1855 61142 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.64 Å2
Refinement stepCycle: LAST / Resolution: 2.29→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 9 207 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213494
X-RAY DIFFRACTIONf_angle_d0.55544764
X-RAY DIFFRACTIONf_chiral_restr0.0424538
X-RAY DIFFRACTIONf_plane_restr0.0043642
X-RAY DIFFRACTIONf_dihedral_angle_d25.6761514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.330.28251290.26312758X-RAY DIFFRACTION99.93
2.33-2.370.26881570.26032781X-RAY DIFFRACTION99.93
2.37-2.410.29551310.25952786X-RAY DIFFRACTION99.97
2.41-2.460.28481560.2432740X-RAY DIFFRACTION99.93
2.46-2.510.27421430.24022736X-RAY DIFFRACTION99.9
2.51-2.560.2921780.2332770X-RAY DIFFRACTION99.93
2.56-2.620.30721450.22692749X-RAY DIFFRACTION100
2.62-2.690.2751230.22082772X-RAY DIFFRACTION99.9
2.69-2.760.26911070.21612815X-RAY DIFFRACTION100
2.76-2.840.21491290.20142804X-RAY DIFFRACTION100
2.84-2.930.22541150.19512782X-RAY DIFFRACTION99.97
2.93-3.040.21861140.20092813X-RAY DIFFRACTION100
3.04-3.160.20341430.19682730X-RAY DIFFRACTION100
3.16-3.30.20611950.17712745X-RAY DIFFRACTION100
3.3-3.480.18331370.17312765X-RAY DIFFRACTION99.93
3.48-3.690.19911300.16192777X-RAY DIFFRACTION99.97
3.69-3.980.15541340.16122791X-RAY DIFFRACTION100
3.98-4.380.14991630.14382754X-RAY DIFFRACTION100
4.38-5.010.17181210.15082786X-RAY DIFFRACTION100
5.01-6.310.19441250.18762793X-RAY DIFFRACTION99.97
6.31-45.270.24691160.18842804X-RAY DIFFRACTION99.66

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