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- PDB-7mrp: MicroED structure of lysozyme from milled crystals at 1.75A -

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Basic information

Entry
Database: PDB / ID: 7mrp
TitleMicroED structure of lysozyme from milled crystals at 1.75A
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.75 Å
AuthorsMartynowycz, M.W. / Gonen, T.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
CitationJournal: To be Published
Title: Preparing crystalline lamellae by focused ion-beam milling for microcrystal electron diffraction (MicroED) experiments
Authors: Martynowycz, M.W. / Gonen, T.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4596
Polymers14,3311
Non-polymers1275
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-45 kcal/mol
Surface area6480 Å2
Unit cell
Length a, b, c (Å)77.620, 77.620, 37.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#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.: 78 / 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: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Lysozyme / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.0143 MDa / Experimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 4.7
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Data collection

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus min: 0 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 85 K / Temperature (min): 77 K
Image recordingAverage exposure time: 1 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of diffraction images: 1500 / Num. of grids imaged: 1 / Num. of real images: 1500
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096
EM diffractionCamera length: 2100 mm / Tilt angle list: -30,30
EM diffraction shellResolution: 1.75→34.18 Å / Fourier space coverage: 100 % / Multiplicity: 25 / Num. of structure factors: 12144 / Phase residual: 18 °
EM diffraction statsFourier space coverage: 100 % / High resolution: 1.75 Å / Num. of intensities measured: 305349 / Num. of structure factors: 12144 / Phase error: 18 ° / Phase residual: 19 ° / Phase error rejection criteria: none / Rmerge: 0.23
ReflectionBiso Wilson estimate: 27.13 Å2

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Processing

Software
NameVersionClassificationNB
phenix.refine1.19_4080refinement
PHENIX1.19_4080refinement
EM software
IDNameCategory
6Cootmodel fitting
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 77.33 Å / B: 77.33 Å / C: 38.11 Å / Space group name: P43212 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 1.75 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Algorithm: FOURIER SPACE / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 25 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: LL
Atomic model buildingPDB-ID: 5K7O

5k7o


Accession code: 5K7O / Source name: PDB / Type: experimental model
RefinementResolution: 1.75→34.04 Å / SU ML: 0.2792 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 1216 10 %
Rwork0.1684 10944 -
obs0.1729 12160 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.35 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 5 78 1084
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00911021
ELECTRON CRYSTALLOGRAPHYf_angle_d1.06511381
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0685144
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0074181
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d6.2221143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.46851310.38191184ELECTRON CRYSTALLOGRAPHY100
1.82-1.90.33981340.22911203ELECTRON CRYSTALLOGRAPHY100
1.9-20.23871320.15461186ELECTRON CRYSTALLOGRAPHY100
2-2.130.23741310.16341185ELECTRON CRYSTALLOGRAPHY100
2.13-2.290.23041340.16631199ELECTRON CRYSTALLOGRAPHY100
2.29-2.520.22031350.16051216ELECTRON CRYSTALLOGRAPHY100
2.52-2.890.2341350.16811218ELECTRON CRYSTALLOGRAPHY100
2.89-3.640.18521370.16331232ELECTRON CRYSTALLOGRAPHY99.93
3.64-34.040.17561470.15391321ELECTRON CRYSTALLOGRAPHY99.93

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