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- PDB-5ocv: A Rare Lysozyme Crystal Form Solved Using High-Redundancy 3D Elec... -

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Entry
Database: PDB / ID: 5ocv
TitleA Rare Lysozyme Crystal Form Solved Using High-Redundancy 3D Electron Diffraction Data from Micron-Sized Needle Shaped Crystals
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme activity
Function / homology
Function and homology information


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 Gram-positive bacterium / defense response to bacterium ...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 Gram-positive bacterium / defense response to 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 / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.2 Å
AuthorsXu, H. / Lebrette, H. / Yang, T. / Srinivas, V. / Hovmoller, S. / Hogbom, M. / Zou, X.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation3DEM-NATUR Sweden
Knut and Alice Wallenberg FoundationWallenberg Academy Fellows Sweden
Science for Life LaboratoryElectron Nanocrystallography Sweden
Swedish Foundation for Strategic Research Sweden
Swedish Research Council Sweden
Wenner-Gren Foundation Sweden
CitationJournal: Structure / Year: 2018
Title: A Rare Lysozyme Crystal Form Solved Using Highly Redundant Multiple Electron Diffraction Datasets from Micron-Sized Crystals.
Authors: Hongyi Xu / Hugo Lebrette / Taimin Yang / Vivek Srinivas / Sven Hovmöller / Martin Högbom / Xiaodong Zou /
Abstract: Recent developments of novel electron diffraction techniques have shown to be powerful for determination of atomic resolution structures from micron- and nano-sized crystals, too small to be studied ...Recent developments of novel electron diffraction techniques have shown to be powerful for determination of atomic resolution structures from micron- and nano-sized crystals, too small to be studied by single-crystal X-ray diffraction. In this work, the structure of a rare lysozyme polymorph is solved and refined using continuous rotation MicroED data and standard X-ray crystallographic software. Data collection was performed on a standard 200 kV transmission electron microscope (TEM) using a highly sensitive detector with a short readout time. The data collection is fast (∼3 min per crystal), allowing multiple datasets to be rapidly collected from a large number of crystals. We show that merging data from 33 crystals significantly improves not only the data completeness, overall I/σ and the data redundancy, but also the quality of the final atomic model. This is extremely useful for electron beam-sensitive crystals of low symmetry or with a preferred orientation on the TEM grid.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6853
Polymers28,6622
Non-polymers231
Water45025
1
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3542
Polymers14,3311
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.720, 103.880, 31.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 33
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: 3D crystals of Lysozyme C from Gallus gallus / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
EM crystal formationAtmosphere: AIR
Details: 2 microliters of Lysozyme (8 mg/ml in 10 mM Tris-HCl pH 8.0) was mixed with 2 microliters of precipitant solution consisting of 1 M potassium nitrate, 0.1 M sodium acetate trihydrate pH 3.4. ...Details: 2 microliters of Lysozyme (8 mg/ml in 10 mM Tris-HCl pH 8.0) was mixed with 2 microliters of precipitant solution consisting of 1 M potassium nitrate, 0.1 M sodium acetate trihydrate pH 3.4. Thin fibrous needle-shaped crystal clusters were grown by the hanging drop vapor diffusion method.
Temperature: 294 K / Time: 2 DAY
Buffer solutionpH: 3.4
Buffer component
IDConc.NameFormulaBuffer-ID
11 Mpotassium nitrateKNO31
20.1 Msodium acetateC2H3NaO21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 167 divisions/in. / Grid type: Okenshoji
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 298 K
Crystal growpH: 3.4

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Data collection

MicroscopyModel: JEOL 2100
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 0.16 e/Å2 / Film or detector model: OTHER
Image scansSampling size: 55 µm / Width: 512 / Height: 512
EM diffractionCamera length: 800 mm
EM diffraction shellResolution: 2.2→28.68 Å / Fourier space coverage: 79.67 % / Multiplicity: 42.4 / Num. of structure factors: 9516 / Phase residual: 1 °
EM diffraction statsDetails: Rmeas: 0.614 Rp.i.m.: 0.082 / Fourier space coverage: 79.67 % / High resolution: 2.2 Å / Num. of intensities measured: 403297 / Num. of structure factors: 9516 / Phase error: 31.3 ° / Phase residual: 1 ° / Phase error rejection criteria: 1 / Rmerge: 0.607 / Rsym: 0.607
DiffractionMean temperature: 97 K
ReflectionResolution: 2.2→28.68 Å / Num. obs: 9516 / % possible obs: 79.7 % / Redundancy: 42.4 %
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 25.9 % / % possible all: 64.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
PHASERphasing
EM software
IDNameVersionCategory
8PHENIX1.11.1model refinement
9Coot0.8.8model refinement
10PHASER2.7.16molecular replacement
13XSCALENov 1, 2016crystallography merging
Image processingDetails: ASI TimePix QTPX-262k
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 67.72 Å / B: 103.88 Å / C: 31.65 Å / Space group name: P21212 / Space group num: 18
CTF correctionType: NONE
3D reconstructionResolution: 2.2 Å / Resolution method: OTHER / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AKI

1aki


Resolution: 2.2→28.673 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3
RfactorNum. reflection% reflectionSelection details
Rfree0.27 476 5 %Random
Rwork0.2365 ---
obs0.2382 9516 79.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.77 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0022054
ELECTRON CRYSTALLOGRAPHYf_angle_d0.552783
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d18.7621223
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.042287
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.003363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.51820.3661270.32652413ELECTRON CRYSTALLOGRAPHY65
2.5182-3.17210.35721710.31433247ELECTRON CRYSTALLOGRAPHY87
3.1721-28.67540.21121780.18313380ELECTRON CRYSTALLOGRAPHY86
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON CRYSTALLOGRAPHY

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)
16.94030.0954-3.59234.6836-1.20847.0996-0.2948-0.62060.021-0.1217-0.0692-0.90560.06290.24060.39380.19170.0681-0.03770.21780.01960.40481.415715.89372.5269
22.37330.2826-0.84212.81820.45828.8346-0.19470.5894-0.0140.1386-0.20920.333-0.3537-0.19840.41280.17020.0480.00330.18190.07150.254181.86387.1540.0008
30.9968-2.1337-0.16334.93640.00030.35840.2592-0.13160.07580.3406-0.14780.6395-0.2484-0.1145-0.05490.3593-0.09750.24730.3437-0.03620.516379.9864-6.290315.6041
42.9576-1.6825-0.9651.1028-0.09423.2828-0.10150.0035-0.3148-0.08990.45430.41360.9746-0.1902-0.28440.3435-0.0288-0.06880.18930.10680.275786.8009-2.651811.7798
54.302-0.27410.2663.0647-2.54373.8376-0.0738-0.0632-0.0539-0.7332-0.00650.2284-0.0210.12420.10460.30180.062-0.04850.1562-0.01330.165791.5730.774812.2309
62.4960.39252.03370.31210.37472.92220.08970.0021-0.18670.03480.1223-0.03850.34410.2481-0.11730.02680.0433-0.35010.1707-0.0240.086291.36084.0882.8775
76.25012.11850.85492.11212.08268.37710.15150.0584-1.23230.15950.0131-0.07880.5994-0.1648-0.02490.3891-0.0022-0.04680.1623-0.02890.427379.1092-1.8217-3.324
82.4961.2774-0.42525.88490.12371.48-0.4878-0.135-0.0385-0.39830.23030.49240.24860.0334-0.0036-0.01260.2061-0.15850.45210.16290.127475.815.2941-6.6331
93.64370.47090.30591.32290.81623.55190.1781-0.01240.25340.09870.2384-0.0897-0.0632-0.0741-0.46480.3145-0.145-0.01730.23660.03240.224661.524117.993312.4372
103.1432-0.08490.96772.95061.18343.0422-0.29230.28620.1472-0.2162-0.0084-0.1972-0.44160.17250.2460.27880.0020.07490.1775-0.01550.17765.979126.342118.2938
116.75993.4648-0.7434.57340.18551.0127-0.08210.56121.26610.14850.31460.2916-0.07140.0101-0.31820.12820.00320.03090.5444-0.0870.353564.406932.76471.4341
127.01594.63613.21799.0406-4.06297.8813-0.46490.53410.101-0.22890.00250.2609-0.25020.54130.35470.21210.1090.0790.4559-0.01630.380768.035931.46054.8666
134.32921.21171.9815.1883-3.26739.308-0.1155-0.50960.559-0.3644-0.0030.53030.0846-0.22710.01470.1730.07820.03920.2097-0.03340.354576.2535.73222.6486
142.9965-2.97873.27953.1442-3.90175.8169-0.05530.19830.441.17450.0739-0.4519-1.23780.83960.21680.6591-0.16120.03770.321-0.03350.266580.985334.24483.9392
156.7193-1.5889-1.05521.7601-1.31161.93970.45310.8424-0.722-0.4791-0.07180.3220.4655-0.3365-0.36730.6674-0.1327-0.07150.4383-0.03270.163471.230723.30522.4419
165.46922.1298-0.08756.00984.27363.59160.51670.4104-0.1580.2980.3631-0.15530.1697-0.1698-0.7520.26040.0076-0.0320.22110.01360.168574.858725.9312.5084
173.48220.30025.02028.61823.41299.1285-0.17460.22550.0713-0.05390.2046-0.5205-0.36260.0934-0.07250.20470.04430.09120.2650.01180.276671.876635.106417.9072
181.7028-1.0528-0.39663.3708-0.40911.3498-0.12010.49510.0339-0.3242-0.5010.2777-0.4554-0.80780.12740.51670.22230.11370.5797-0.10.04861.473737.289416.5919
196.3438-1.06053.40190.38840.38376.1442-0.0928-0.8418-0.59520.58350.13470.28841.5836-0.4177-0.08171.03460.01680.02320.3579-0.00440.049257.94230.206323.8585
202.64031.47251.09895.00571.72064.0879-0.21810.0194-0.26120.1056-0.37420.1118-0.1310.07860.2710.3924-0.34250.1670.5199-0.02170.369755.976118.179120.7754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON CRYSTALLOGRAPHY1chain 'B' and (resid 1 through 14 )
2ELECTRON CRYSTALLOGRAPHY2chain 'B' and (resid 15 through 42 )
3ELECTRON CRYSTALLOGRAPHY3chain 'B' and (resid 43 through 50 )
4ELECTRON CRYSTALLOGRAPHY4chain 'B' and (resid 51 through 68 )
5ELECTRON CRYSTALLOGRAPHY5chain 'B' and (resid 69 through 88 )
6ELECTRON CRYSTALLOGRAPHY6chain 'B' and (resid 89 through 99 )
7ELECTRON CRYSTALLOGRAPHY7chain 'B' and (resid 100 through 119 )
8ELECTRON CRYSTALLOGRAPHY8chain 'B' and (resid 120 through 129 )
9ELECTRON CRYSTALLOGRAPHY9chain 'A' and (resid 1 through 14 )
10ELECTRON CRYSTALLOGRAPHY10chain 'A' and (resid 15 through 36 )
11ELECTRON CRYSTALLOGRAPHY11chain 'A' and (resid 37 through 50 )
12ELECTRON CRYSTALLOGRAPHY12chain 'A' and (resid 51 through 58 )
13ELECTRON CRYSTALLOGRAPHY13chain 'A' and (resid 59 through 68 )
14ELECTRON CRYSTALLOGRAPHY14chain 'A' and (resid 69 through 78 )
15ELECTRON CRYSTALLOGRAPHY15chain 'A' and (resid 79 through 88 )
16ELECTRON CRYSTALLOGRAPHY16chain 'A' and (resid 89 through 99 )
17ELECTRON CRYSTALLOGRAPHY17chain 'A' and (resid 100 through 108 )
18ELECTRON CRYSTALLOGRAPHY18chain 'A' and (resid 109 through 114 )
19ELECTRON CRYSTALLOGRAPHY19chain 'A' and (resid 115 through 122 )
20ELECTRON CRYSTALLOGRAPHY20chain 'A' and (resid 123 through 129 )

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