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- PDB-8gqb: Crystal structure of lasso peptide epimerase MslH D11A mutant -

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Basic information

Entry
Database: PDB / ID: 8gqb
TitleCrystal structure of lasso peptide epimerase MslH D11A mutant
ComponentsPoly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
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 / DI(HYDROXYETHYL)ETHER / Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)47,6365
Polymers47,2751
Non-polymers3604
Water2,288127
1
A: Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)381,08740
Polymers378,2038
Non-polymers2,88332
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 area41010 Å2
ΔGint-152 kcal/mol
Surface area120150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.115, 127.115, 170.648
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-655-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47275.391 Da / Num. of mol.: 1 / Mutation: D11A
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

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Non-polymers , 5 types, 131 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5.00 mg/mL MslH D11A, 200 mM magnesium chloride, 100 mM Tris-HCl, 20% (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 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→44.94 Å / Num. obs: 51614 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 43.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Net I/σ(I): 16.3
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 15.3 % / Rmerge(I) obs: 1.425 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2833 / CC1/2: 0.86 / % 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: 2.41→44.94 Å / SU ML: 0.2998 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.8968
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 2662 5.16 %
Rwork0.1958 48952 -
obs0.1973 51614 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.39 Å2
Refinement stepCycle: LAST / Resolution: 2.41→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 0 127 3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193426
X-RAY DIFFRACTIONf_angle_d0.48494669
X-RAY DIFFRACTIONf_chiral_restr0.041527
X-RAY DIFFRACTIONf_plane_restr0.0046628
X-RAY DIFFRACTIONf_dihedral_angle_d21.90821260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.450.31651250.29542604X-RAY DIFFRACTION100
2.45-2.50.32181300.29492586X-RAY DIFFRACTION99.96
2.5-2.550.39151440.29452555X-RAY DIFFRACTION99.89
2.55-2.610.31751460.26222552X-RAY DIFFRACTION99.96
2.61-2.670.30561180.2612601X-RAY DIFFRACTION99.85
2.67-2.730.25171490.23882588X-RAY DIFFRACTION100
2.74-2.810.31811410.23792602X-RAY DIFFRACTION100
2.81-2.890.24021290.23492550X-RAY DIFFRACTION99.96
2.89-2.980.30411200.23352578X-RAY DIFFRACTION99.85
2.98-3.090.23681180.22872628X-RAY DIFFRACTION100
3.09-3.210.29091480.2112559X-RAY DIFFRACTION99.93
3.22-3.360.23261420.19362574X-RAY DIFFRACTION100
3.36-3.540.21871280.19222590X-RAY DIFFRACTION99.93
3.54-3.760.19571330.17992587X-RAY DIFFRACTION100
3.76-4.050.19981480.16872552X-RAY DIFFRACTION100
4.05-4.460.18191550.15232567X-RAY DIFFRACTION100
4.46-5.10.1561370.1482583X-RAY DIFFRACTION100
5.1-6.420.21321910.19342536X-RAY DIFFRACTION100
6.43-44.940.1981600.17662560X-RAY DIFFRACTION99.85
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)
11.131939969150.806143873841-0.133045050950.666697218836-0.1861190974311.780246636360.06154288392830.08803389399250.0991802142005-0.0316317343556-0.040583888192-0.0287514005308-0.331382077969-0.0520001309986-0.002457374378630.475960628974-0.00461387262380.02723292791460.384837574930.05852268499380.38163055456825.226977199628.022138158847.8599444829
21.36808995460.0405824453487-0.251286208890.805184230226-0.02353263978032.087909203150.05259945598350.0339723392816-0.0478289478466-0.0177072219236-0.05101617991110.0644977591027-0.233575499339-0.120229288602-0.01090948098930.348966371656-0.02787598098640.00412584447350.3506146454130.02608830211530.35305040257915.666772129417.07375602361.135420833
30.6366096937490.0513958288014-0.259824662550.9833701971820.0563692199550.6483896664010.0528136003469-0.1623296956840.0270572002640.169427164164-0.067942314174-0.07789079892360.0544333114940.1912861523060.01429203455450.345828119925-0.0136725865135-0.0004075920691490.3768286254950.02941295811530.3379047244430.193474152818.377109640979.4368897798
40.9705356809440.1475492306610.05021138973650.4775379458680.1086607647191.124265465390.0124652822919-0.09460394583370.1889340196360.0685571857552-0.0471177208522-0.0436406311481-0.1419991664240.09347951411880.05178102378430.36674504061-0.03998298449470.02636833880920.3656769941920.03657373406740.37315876928929.577815354824.09967666566.1563183647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 387 through 439 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 386 )

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