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- PDB-8b2h: Muramidase from Thermothielavioides terrestris, catalytic domain -

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Basic information

Entry
Database: PDB / ID: 8b2h
TitleMuramidase from Thermothielavioides terrestris, catalytic domain
ComponentsSH3b domain-containing protein
KeywordsHYDROLASE / SH3-like / muramidase / peptidoglycan / cell wall binding domain
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesThermothielavioides terrestris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0554
Polymers23,8621
Non-polymers1933
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.616, 84.616, 62.882
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-303-

ZN

21A-438-

HOH

31A-440-

HOH

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Components

#1: Protein SH3b domain-containing protein


Mass: 23861.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothielavioides terrestris (fungus)
Strain: ATCC 38088 / NRRL 8126 / Gene: THITE_2110902 / Production host: Aspergillus oryzae (mold) / References: UniProt: G2QV10
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PACT screen condition D12 (0.01 M zinc chloride, 0.1 M Tris pH 8, 20% w/v PEG 6000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.36→36.64 Å / Num. obs: 10659 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.051 / Rrim(I) all: 0.133 / Χ2: 1.04 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.83-36.6411.50.06933.52190.9990.0320.0771.1398.9
2.36-2.4512.91.2151.611060.870.5051.3190.8899.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0352refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B2E

8b2e


Resolution: 2.36→36.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 8.739 / SU ML: 0.173 / Cross valid method: FREE R-VALUE / ESU R: 0.206 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2207 492 4.622 %
Rwork0.1971 10153 -
all0.198 --
obs-10645 99.906 %
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: 63.097 Å2
Baniso -1Baniso -2Baniso -3
1-2.569 Å21.285 Å20 Å2
2--2.569 Å2-0 Å2
3----8.335 Å2
Refinement stepCycle: LAST / Resolution: 2.36→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 6 40 1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121080
X-RAY DIFFRACTIONr_bond_other_d0.0010.016973
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.6441454
X-RAY DIFFRACTIONr_angle_other_deg0.3071.5652265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2955142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.42256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17510162
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.6651044
X-RAY DIFFRACTIONr_chiral_restr0.0440.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_nbd_refined0.2230.2234
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.2888
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2546
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.29
X-RAY DIFFRACTIONr_nbd_other0.1750.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0480.24
X-RAY DIFFRACTIONr_mcbond_it2.8696.73571
X-RAY DIFFRACTIONr_mcbond_other2.8656.729571
X-RAY DIFFRACTIONr_mcangle_it4.28410.094712
X-RAY DIFFRACTIONr_mcangle_other4.28110.096713
X-RAY DIFFRACTIONr_scbond_it3.3836.966509
X-RAY DIFFRACTIONr_scbond_other3.2316.966508
X-RAY DIFFRACTIONr_scangle_it4.86110.344742
X-RAY DIFFRACTIONr_scangle_other4.85810.346743
X-RAY DIFFRACTIONr_lrange_it6.36580.9571202
X-RAY DIFFRACTIONr_lrange_other6.35280.9481201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.4210.466360.345750X-RAY DIFFRACTION99.7462
2.421-2.4870.379380.371715X-RAY DIFFRACTION99.7351
2.487-2.5590.426290.326699X-RAY DIFFRACTION100
2.559-2.6370.282300.32704X-RAY DIFFRACTION99.8639
2.637-2.7230.299230.284661X-RAY DIFFRACTION99.7085
2.723-2.8180.39340.282643X-RAY DIFFRACTION100
2.818-2.9240.28200.242633X-RAY DIFFRACTION100
2.924-3.0430.244190.231598X-RAY DIFFRACTION100
3.043-3.1770.224360.249572X-RAY DIFFRACTION100
3.177-3.3310.251290.227542X-RAY DIFFRACTION100
3.331-3.5090.308280.213535X-RAY DIFFRACTION100
3.509-3.720.211340.195470X-RAY DIFFRACTION100
3.72-3.9740.178210.18467X-RAY DIFFRACTION100
3.974-4.2880.165320.158435X-RAY DIFFRACTION100
4.288-4.6910.192220.145398X-RAY DIFFRACTION100
4.691-5.2340.232200.157366X-RAY DIFFRACTION100
5.234-6.0240.208120.182328X-RAY DIFFRACTION100
6.024-7.3280.159160.134273X-RAY DIFFRACTION100
7.328-10.1630.085100.11224X-RAY DIFFRACTION100
10.163-36.640.12930.171141X-RAY DIFFRACTION100

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