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- PDB-6h9d: Muramidase domain of SpmX from Asticaccaulis excentricus -

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Basic information

Entry
Database: PDB / ID: 6h9d
TitleMuramidase domain of SpmX from Asticaccaulis excentricus
ComponentsLysozyme
KeywordsHYDROLASE / lysozyme / peptidoglycan hydrolase / cell morphogenesis / stalk synthesis
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / host cell cytoplasm / defense response to bacterium / membrane
Similarity search - Function
Endolysin/autolysin / : / Lysozyme - #40 / Endolysin T4 type / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAsticcacaulis excentricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRandich, A.M. / Morlot, C.M. / Brun, Y.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM051986 United States
CitationJournal: Curr.Biol. / Year: 2019
Title: Origin of a Core Bacterial Gene via Co-option and Detoxification of a Phage Lysin.
Authors: Randich, A.M. / Kysela, D.T. / Morlot, C. / Brun, Y.V.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2236
Polymers50,0033
Non-polymers2203
Water2,864159
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7953
Polymers16,6681
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7602
Polymers16,6681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme


Theoretical massNumber of molelcules
Total (without water)16,6681
Polymers16,6681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.440, 100.440, 96.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-202-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 149
2010B2 - 149
1020A3 - 148
2020C3 - 148
1030B3 - 148
2030C3 - 148

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Lysozyme / Muramidase domain of SpmX


Mass: 16667.811 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asticcacaulis excentricus (bacteria) / Gene: Astex_1112 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: E8RMG8, lysozyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.34 % / Description: Large 3D needles
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5 0.2 M MgCl2 12% PEG 3350 / PH range: 8.3-8.7

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.9→44.56 Å / Num. obs: 42611 / % possible obs: 95.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 44.4 Å2 / Rsym value: 0.02 / Net I/σ(I): 33.99
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 6805 / Rsym value: 0.436 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANX

2anx


Resolution: 1.9→44.56 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.75 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25594 4288 10.1 %RANDOM
Rwork0.21141 ---
obs0.21594 38321 95.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å2-0 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 13 160 3657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0143566
X-RAY DIFFRACTIONr_bond_other_d00.0173150
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.6524824
X-RAY DIFFRACTIONr_angle_other_deg0.9431.6337375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68120.811222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58715588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3881539
X-RAY DIFFRACTIONr_chiral_restr0.0580.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024110
X-RAY DIFFRACTIONr_gen_planes_other00.02678
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5224.0591771
X-RAY DIFFRACTIONr_mcbond_other4.5194.0581770
X-RAY DIFFRACTIONr_mcangle_it5.4716.0642209
X-RAY DIFFRACTIONr_mcangle_other5.476.0652210
X-RAY DIFFRACTIONr_scbond_it5.9274.6321795
X-RAY DIFFRACTIONr_scbond_other5.9264.6341796
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9246.7382614
X-RAY DIFFRACTIONr_long_range_B_refined8.58447.6214015
X-RAY DIFFRACTIONr_long_range_B_other8.59647.5563992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A4745
12B4745
21A4744
22C4744
31B4653
32C4653
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 280 -
Rwork0.39 2774 -
obs--94.03 %

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