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- PDB-5o6q: High pressure flash cooled hen egg white lysozyme -

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Basic information

Entry
Database: PDB / ID: 5o6q
TitleHigh pressure flash cooled hen egg white lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / high pressure flash cooling / crystal grown without cryoprotectants
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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsThielmann, Y. / Quirnheim Pais, D.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: A standardized technique for high-pressure cooling of protein crystals.
Authors: Quirnheim Pais, D. / Rathmann, B. / Koepke, J. / Tomova, C. / Wurzinger, P. / Thielmann, Y.
History
DepositionJun 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5557
Polymers14,3311
Non-polymers2246
Water2,432135
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-53 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.950, 77.950, 37.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-342-

HOH

31A-432-

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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: lysozyme was dissolved in 0.02 M sodium acetate pH 4.6 to yield 20 mg/ml and mixed 1:1 with 0.8 M sodium chloride and 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→38.98 Å / Num. obs: 20967 / % possible obs: 99.9 % / Redundancy: 24.9 % / Rmerge(I) obs: 0.04809 / Rrim(I) all: 0.04913 / Net I/σ(I): 34.46
Reflection shellResolution: 1.449→1.501 Å / Rmerge(I) obs: 1.856 / Rrim(I) all: 1.897

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vb1

2vb1


Resolution: 1.45→38.975 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.65
RfactorNum. reflection% reflection
Rfree0.1968 1970 9.57 %
Rwork0.1724 --
obs0.1748 20592 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→38.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 9 135 1144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051081
X-RAY DIFFRACTIONf_angle_d0.7521475
X-RAY DIFFRACTIONf_dihedral_angle_d12.048414
X-RAY DIFFRACTIONf_chiral_restr0.078153
X-RAY DIFFRACTIONf_plane_restr0.005195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.449-1.48520.3181300.30141209X-RAY DIFFRACTION91
1.4852-1.52540.30311320.26231244X-RAY DIFFRACTION95
1.5254-1.57030.25111370.22541289X-RAY DIFFRACTION96
1.5703-1.6210.23991370.21941292X-RAY DIFFRACTION97
1.621-1.67890.27761350.19411294X-RAY DIFFRACTION98
1.6789-1.74610.23651400.21031327X-RAY DIFFRACTION99
1.7461-1.82560.27161400.19861315X-RAY DIFFRACTION99
1.8256-1.92180.2391410.19121340X-RAY DIFFRACTION100
1.9218-2.04220.21311440.19091353X-RAY DIFFRACTION100
2.0422-2.19990.22641420.17091350X-RAY DIFFRACTION100
2.1999-2.42130.20251430.17711350X-RAY DIFFRACTION100
2.4213-2.77150.20791460.18631380X-RAY DIFFRACTION100
2.7715-3.49150.17851460.1631394X-RAY DIFFRACTION100
3.4915-38.98910.1561570.14361485X-RAY DIFFRACTION100
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)
12.09330.8213-1.22945.7636-1.18470.8258-0.43160.2561-0.4375-0.87040.1795-0.23950.53060.19390.06670.4697-0.0050.12190.2139-0.07170.3241-16.041-7.3567-18.1508
23.1559-3.14531.07947.4831.09011.57990.0417-0.107-0.6409-0.206-0.07170.25230.52680.13970.05020.4103-0.02070.08810.18670.04690.3094-23.4099-11.9735-7.695
36.81413.7592-0.9462.2619-0.88081.2507-0.15630.0254-0.1434-0.18070.0614-0.02530.1528-0.10180.10380.2824-0.01710.02440.1787-0.03060.2329-21.63340.1889-15.0398
49.20983.475-1.09012.8539-0.01443.23450.1296-0.3790.6931-0.0609-0.00410.1098-0.0968-0.9242-0.09340.22540.0440.0480.2539-0.02350.266-19.291114.7347-4.3008
57.53692.74451.14593.5755-2.02482.51040.0586-0.50530.02660.2766-0.15770.03090.2665-0.11410.0710.2158-0.01150.04290.20750.00020.1872-16.22417.316-2.1481
65.4771-0.2043-2.11912.8892.84423.48080.1811-0.9531-0.36941.0851-0.44310.00420.445-0.18960.25560.4195-0.0528-0.00110.430.03690.2179-13.72494.76954.8999
77.69294.6712-1.09853.8223-0.19690.9302-0.0762-0.1168-0.6532-0.1211-0.1359-0.42820.2690.1260.23910.2670.04630.04710.19150.04580.2961-13.2086-2.1641-6.0457
83.5764-1.452.96047.9553-6.04089.78620.0244-0.47910.16110.5184-0.21460.2062-0.4315-0.14110.18190.3329-0.01380.0430.2825-0.0140.2846-29.16370.0615-5.3593
98.2193-6.1463-6.03796.29127.18398.6555-0.22280.6528-1.0071-0.1562-0.22830.55680.8135-0.60720.51320.4887-0.10840.00150.2387-0.06660.3478-28.4984-8.5669-19.6187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 99 )
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 114 )
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 129 )

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