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- PDB-7f26: Crystal structure of lysozyme -

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Basic information

Entry
Database: PDB / ID: 7f26
TitleCrystal structure of lysozyme
ComponentsLysozyme C
KeywordsPROTEIN BINDING / lysozyme
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
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-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiang, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Novel combined crystallization plate for high-throughput crystal screening and in situ data collection at a crystallography beamline.
Authors: Liang, M. / Yu, L. / Wang, Z. / Zhou, H. / Zhang, Y. / Wang, Q. / He, J.
History
DepositionJun 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6500 Å2
Unit cell
Length a, b, c (Å)78.942, 78.942, 37.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

21A-278-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M citric acid and 0.2M sodium acetate were mixed in a ratio of 1:1 to form a buffer solution, and the buffer solution was mixed with 12%-16% sodium chloride in a ratio of 1:1 to form the mother liquor

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→39.47 Å / Num. obs: 13336 / % possible obs: 97.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.082 / Rrim(I) all: 0.195 / Net I/σ(I): 7.3 / Num. measured all: 64515 / Scaling rejects: 173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.733.30.43323026900.7940.2590.5093.195.2
9-39.474.10.1184701140.9740.0580.13310.994.6

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RCM

1rcm


Resolution: 1.7→27.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 1331 10 %
Rwork0.1655 11977 -
obs0.1688 13308 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.85 Å2 / Biso mean: 20.5362 Å2 / Biso min: 6.05 Å2
Refinement stepCycle: final / Resolution: 1.7→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 0 105 1105
Biso mean---32.87 -
Num. residues----129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.76080.27411270.2106114394
1.7608-1.83130.20971280.1972115796
1.8313-1.91460.2261320.1654117998
1.9146-2.01550.21881330.156120399
2.0155-2.14170.17541340.1559120198
2.1417-2.3070.18781310.1555118497
2.307-2.53910.18141330.1671120398
2.5391-2.90610.20511330.1802119396
2.9061-3.66010.18951360.1631122097
3.6601-27.910.19361440.1559129496
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

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)
11.12570.7413-0.48432.7515-0.4821.9466-0.27790.2038-0.4645-0.42350.1-0.56710.18850.2155-0.060.1695-0.01340.07310.1364-0.06810.1966-16.3823-6.7192-18.9683
26.2244-0.9732-0.18761.73320.54460.4506-0.228-0.1324-0.5074-0.02820.066-0.02540.16380.160.06630.21450.00720.06720.07930.01780.1739-23.8083-11.815-8.0437
31.8550.95240.18581.08260.61070.4406-0.19380.11220.017-0.19190.13940.0023-0.02320.01530.06550.0913-0.02720.01520.0988-0.02260.0947-21.77910.3895-15.6704
42.1829-1.7914-3.2663.55112.9828.8070.1348-0.24840.37790.176-0.05320.1695-0.5381-0.32750.02840.1943-0.00180.0280.1502-0.05180.1619-19.944414.5937-4.7302
51.45120.30680.29162.2308-0.35741.26840.0925-0.25820.06190.2401-0.1656-0.01610.0084-0.16830.07550.1285-0.04890.00860.1373-0.02030.086-16.88757.0143-2.5288
61.1441-0.6495-0.87016.58722.11721.42260.1985-0.4291-0.02520.6656-0.203-0.13310.16440.0923-0.01610.2234-0.0706-0.03910.2280.01020.1049-14.32414.93974.5658
70.6980.90970.27021.72491.44532.57280.05550.0492-0.2376-0.0965-0.0834-0.3259-0.06780.2279-0.0350.1341-0.00850.02110.14980.00060.142-9.66521.434-8.8126
84.2640.58-2.01972.2046-0.08012.9342-0.0938-0.1637-0.57610.1427-0.062-0.22630.33950.03130.08710.154-0.0029-0.01450.1250.0270.1549-17.8256-5.262-3.5401
92.9787-0.06630.44113.8002-1.96592.96630.0711-0.2720.09670.1014-0.06460.2544-0.40270.01170.03310.14580.01010.02630.1006-0.01280.1135-29.94670.6194-6.6786
102.3565-2.6473-2.35363.56772.79233.64750.04270.4261-0.5699-0.2004-0.04310.15960.2581-0.22150.0420.1993-0.0327-0.01590.1898-0.10220.2521-28.4991-8.6524-20.3357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )A15 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 42 )A25 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )A43 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 68 )A51 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )A69 - 78
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 88 )A79 - 88
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 100 )A89 - 100
9X-RAY DIFFRACTION9chain 'A' and (resid 101 through 114 )A101 - 114
10X-RAY DIFFRACTION10chain 'A' and (resid 115 through 129 )A115 - 129

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