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- PDB-8b2g: SH3-like domain from Penicillium virgatum muramidase -

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Basic information

Entry
Database: PDB / ID: 8b2g
TitleSH3-like domain from Penicillium virgatum muramidase
ComponentsSH3b domain-containing protein
KeywordsHYDROLASE / SH3-like / muramidase / peptidoglycan / cell wall binding domain
Function / homologySH3 Domains / SH3 type barrels. / Roll / Mainly Beta
Function and homology information
Biological speciesPenicillium virgatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 13, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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: SH3b domain-containing protein
B: SH3b domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8977
Polymers15,5832
Non-polymers3145
Water1,76598
1
A: SH3b domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9814
Polymers7,7921
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3b domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9163
Polymers7,7921
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.142, 59.824, 36.109
Angle α, β, γ (deg.)90.000, 112.131, 90.000
Int Tables number4
Space group name H-MP1211
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: ASP / End label comp-ID: ASP / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 74 / Label seq-ID: 1 - 74

Dom-ID
1
2

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

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Components

#1: Protein SH3b domain-containing protein


Mass: 7791.546 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium virgatum (fungus) / Production host: Aspergillus oryzae (mold)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PACT C9=0.2 M LiCl, 0.1 M Hepes pH 7.0, 20% PEG 6K, MMS (microseed matrix screening) from JCSG, C7=0.2 M zinc acetate dehydrate, 0.1 M sodium acetate, 10%w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28249 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28249 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7624
pseudo-merohedral22-L, -K, -H20.2376
ReflectionResolution: 1.5→59.82 Å / Num. obs: 21381 / % possible obs: 93.8 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.069 / Rrim(I) all: 0.108 / Χ2: 0.96 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.22-59.823.80.04618.31550.9950.040.0610.7198.9
1.5-1.533.20.96717310.2610.8351.2821.1266.8

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0352refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B2S

8b2s


Resolution: 1.5→33.479 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.697 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.015 / ESU R Free: 0.014
Details: Hydrogens have been added in their riding positions twin refinement using structure amplitudes
RfactorNum. reflection% reflection
Rfree0.1725 1052 4.925 %
Rwork0.1631 20307 -
all0.164 --
obs-21359 93.218 %
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: 16.849 Å2
Baniso -1Baniso -2Baniso -3
1--3.759 Å2-0 Å22.023 Å2
2--3.359 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 17 98 1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121139
X-RAY DIFFRACTIONr_bond_other_d0.0010.016978
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6631551
X-RAY DIFFRACTIONr_angle_other_deg0.5651.5712287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.71752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.55810158
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3351042
X-RAY DIFFRACTIONr_chiral_restr0.0820.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_nbd_refined0.2120.2181
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2897
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2579
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.262
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0310.22
X-RAY DIFFRACTIONr_nbd_other0.1180.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.211
X-RAY DIFFRACTIONr_mcbond_it1.9971.703600
X-RAY DIFFRACTIONr_mcbond_other1.9981.701600
X-RAY DIFFRACTIONr_mcangle_it2.8672.55750
X-RAY DIFFRACTIONr_mcangle_other2.8852.553751
X-RAY DIFFRACTIONr_scbond_it2.7351.922539
X-RAY DIFFRACTIONr_scbond_other2.7331.924540
X-RAY DIFFRACTIONr_scangle_it3.8952.778801
X-RAY DIFFRACTIONr_scangle_other3.8932.78802
X-RAY DIFFRACTIONr_lrange_it4.76834.7074882
X-RAY DIFFRACTIONr_lrange_other4.70734.2634836
X-RAY DIFFRACTIONr_ncsr_local_group_10.0930.052243
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.093070.0501
12AX-RAY DIFFRACTIONLocal ncs0.093070.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5370.344510.2731058X-RAY DIFFRACTION66.0119
1.537-1.5790.254740.2271378X-RAY DIFFRACTION88.8073
1.579-1.6250.216570.21459X-RAY DIFFRACTION93.4649
1.625-1.6750.255690.1981355X-RAY DIFFRACTION93.0719
1.675-1.730.217660.1861347X-RAY DIFFRACTION93.8247
1.73-1.790.215690.181297X-RAY DIFFRACTION94.7953
1.79-1.8580.181740.1581248X-RAY DIFFRACTION94.2939
1.858-1.9330.16600.1371250X-RAY DIFFRACTION95.7602
1.933-2.0190.148550.1461188X-RAY DIFFRACTION95.3221
2.019-2.1170.2720.1571137X-RAY DIFFRACTION96.4884
2.117-2.2310.16550.1611079X-RAY DIFFRACTION96.8403
2.231-2.3660.143440.1451030X-RAY DIFFRACTION97.019
2.366-2.5280.206610.161959X-RAY DIFFRACTION97.3282
2.528-2.730.15570.156909X-RAY DIFFRACTION97.5758
2.73-2.9880.123430.145841X-RAY DIFFRACTION97.6796
2.988-3.3380.164500.156779X-RAY DIFFRACTION98.4561
3.338-3.8480.124440.154652X-RAY DIFFRACTION98.8636
3.848-4.6970.188220.134600X-RAY DIFFRACTION99.0446
4.697-6.5780.214170.193470X-RAY DIFFRACTION99.1853
6.578-33.4790.145120.222271X-RAY DIFFRACTION98.951

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