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- PDB-8b2s: GH24 family muramidase from Trichophaea saccata with an SH3-like ... -

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Basic information

Entry
Database: PDB / ID: 8b2s
TitleGH24 family muramidase from Trichophaea saccata with an SH3-like cell wall binding domain
ComponentsGH24 family muramidase
KeywordsHYDROLASE / SH3-like / muramidase / peptidoglycan / cell wall binding domain
Function / homology:
Function and homology information
Biological speciesTrichophaea saccata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMoroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Nymand-Grarup, S. / Ming, L. / Ye, L. ...Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Nymand-Grarup, S. / Ming, L. / Ye, L. / Klausen, M. / Cohn, M.T. / Schmidt, E.G.W. / Davies, G.J. / Wilson, K.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Module walking using an SH3-like cell-wall-binding domain leads to a new GH184 family of muramidases.
Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Friis, E.P. / Nymand-Grarup, S. / Ming, L. / Ye, L. / Klausen, M. / Cohn, M.T. / Schmidt, ...Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Skov, L.K. / Pache, R.A. / Schnorr, K.M. / Kiemer, L. / Friis, E.P. / Nymand-Grarup, S. / Ming, L. / Ye, L. / Klausen, M. / Cohn, M.T. / Schmidt, E.G.W. / Davies, G.J. / Wilson, K.S.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH24 family muramidase
B: GH24 family muramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5724
Polymers52,4942
Non-polymers782
Water6,359353
1
A: GH24 family muramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2862
Polymers26,2471
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH24 family muramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2862
Polymers26,2471
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.438, 99.438, 133.254
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: CYS / End label comp-ID: CYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 245 / Label seq-ID: 1 - 245

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein GH24 family muramidase


Mass: 26246.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichophaea saccata (fungus) / Production host: Aspergillus oryzae (mold)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 1.84 Å3/Da / Density % sol: 33.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: AmSO4 screen (Qiagen), condition C3: 0.2 M potassium fluoride, 2.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.94→46.582 Å / Num. obs: 56987 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 32.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.04 / Rrim(I) all: 0.083 / Χ2: 1.01 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.1-46.586.60.02950.26310.9990.0160.0341.1999.3
1.94-1.998.52.2630.937970.3281.2322.5820.89100

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data reduction
Aimlessdata scaling
BALBESphasing
REFMAC5.8.0352refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HDE

1hde


Resolution: 1.94→46.582 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.569 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2013 2862 5.027 %
Rwork0.168 54075 -
all0.17 --
obs-56937 99.981 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.129 Å20.064 Å20 Å2
2--0.129 Å2-0 Å2
3----0.417 Å2
Refinement stepCycle: LAST / Resolution: 1.94→46.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 2 353 3965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123758
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163369
X-RAY DIFFRACTIONr_angle_refined_deg1.541.665118
X-RAY DIFFRACTIONr_angle_other_deg0.5361.5617904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.594514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27810590
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.6410139
X-RAY DIFFRACTIONr_chiral_restr0.0770.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024233
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02699
X-RAY DIFFRACTIONr_nbd_refined0.2060.2704
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.22847
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21884
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2279
X-RAY DIFFRACTIONr_metal_ion_refined0.4010.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1180.223
X-RAY DIFFRACTIONr_nbd_other0.2040.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.224
X-RAY DIFFRACTIONr_mcbond_it2.5113.0741927
X-RAY DIFFRACTIONr_mcbond_other2.5123.0741927
X-RAY DIFFRACTIONr_mcangle_it3.2224.5942409
X-RAY DIFFRACTIONr_mcangle_other3.2214.5952410
X-RAY DIFFRACTIONr_scbond_it4.1923.3951831
X-RAY DIFFRACTIONr_scbond_other4.1913.3961832
X-RAY DIFFRACTIONr_scangle_it4.9064.9362708
X-RAY DIFFRACTIONr_scangle_other4.9054.9372709
X-RAY DIFFRACTIONr_lrange_it6.23463.14116187
X-RAY DIFFRACTIONr_lrange_other6.15861.75615921
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.057562
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.065690.05009
12AX-RAY DIFFRACTIONLocal ncs0.065690.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.3362120.3273955X-RAY DIFFRACTION99.952
1.99-2.0450.3131940.2883844X-RAY DIFFRACTION100
2.045-2.1040.2261850.253768X-RAY DIFFRACTION100
2.104-2.1690.2432130.2283599X-RAY DIFFRACTION100
2.169-2.240.2061800.2073545X-RAY DIFFRACTION100
2.24-2.3180.261630.23435X-RAY DIFFRACTION100
2.318-2.4050.2361870.1863289X-RAY DIFFRACTION100
2.405-2.5030.2081680.1763170X-RAY DIFFRACTION100
2.503-2.6140.2611740.1933061X-RAY DIFFRACTION100
2.614-2.7410.2241390.1782928X-RAY DIFFRACTION100
2.741-2.8890.2161730.1862768X-RAY DIFFRACTION100
2.889-3.0640.2221200.1842671X-RAY DIFFRACTION100
3.064-3.2740.2111570.182457X-RAY DIFFRACTION100
3.274-3.5350.1681180.1552337X-RAY DIFFRACTION100
3.535-3.870.1851100.1382153X-RAY DIFFRACTION99.9117
3.87-4.3230.1461050.1171965X-RAY DIFFRACTION100
4.323-4.9850.143870.1161744X-RAY DIFFRACTION100
4.985-6.0880.2840.1481470X-RAY DIFFRACTION100
6.088-8.5370.173600.1521188X-RAY DIFFRACTION100
8.537-46.5820.223330.185728X-RAY DIFFRACTION99.8688
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)
13.11530.3040.85652.72220.18365.11390.12520.0501-0.2965-0.1353-0.00290.02370.29190.1082-0.12220.04310.0146-0.05940.0295-0.0540.1792-59.822-40.66826.202
23.0291-0.4759-0.68082.30790.15493.0128-0.1819-0.136-0.03330.16170.0232-0.16720.28180.0660.15880.0571-0.0220.00360.06660.00510.0221-63.749-38.723-5.41
32.87040.5845-0.90233.43810.36044.54670.13640.16120.045-0.0663-0.1050.094-0.3164-0.3053-0.03150.14380.05170.00540.0336-0.00210.0459-57.284-15.55427.94
41.23020.53140.41562.7696-0.23312.4801-0.10790.07960.0866-0.17010.0082-0.0967-0.2016-0.12750.09970.0536-0.01620.00230.0404-0.00330.0191-61.76-16.32259.308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 73
2X-RAY DIFFRACTION2ALLA79 - 245

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