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- PDB-6muz: Lysozyme, room temperature structure solved by serial 3 degree os... -

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Basic information

Entry
Database: PDB / ID: 6muz
TitleLysozyme, room temperature structure solved by serial 3 degree oscillation crystallography
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 / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsFinke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Kriksunov, I. / Gruner, S.M. / Miller, R.J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: IUCrJ / Year: 2019
Title: Fixed-target serial oscillation crystallography at room temperature.
Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / Szebenyi, D.M.E. / Gruner, S.M. / Miller, R.J.D. / Finke, A.D.
History
DepositionOct 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

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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)14,4254
Polymers14,3311
Non-polymers943
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.100, 79.100, 38.020
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-321-

HOH

21A-335-

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: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 50 mg/ml Lysozyme solution (in deionized H2O) was used for crystallization. A mixture of 1 mL of Lysozyme sample and 3 mL of precipitant (20% w/v NaCl, 6% PEG 6K, 0.5 M NaOAc pH 4.0)

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.2155 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 3, 2018 / Details: Be compound refractive lens
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2155 Å / Relative weight: 1
ReflectionResolution: 1.839→39.55 Å / Num. obs: 10841 / % possible obs: 98.87 % / Redundancy: 10.01 % / CC1/2: 0.991 / Rrim(I) all: 0.3388 / Net I/σ(I): 10.01
Reflection shellResolution: 1.839→1.905 Å / Num. unique obs: 981 / CC1/2: 0.352
Serial crystallography sample deliveryDescription: fixed target Si microchips / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Si microchips / Details: 3 degree oscillation per well / Sample holding: wells / Sample unit size: 20 µm / Support base: goniometer
Serial crystallography data reductionCrystal hits: 975 / Frame hits: 14625 / Frames indexed: 7620 / Frames total: 60600

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPX

1dpx


Resolution: 1.839→39.55 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.17
RfactorNum. reflection% reflection
Rfree0.2036 541 4.99 %
Rwork0.1703 --
obs0.172 10839 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.839→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 39 1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061040
X-RAY DIFFRACTIONf_angle_d0.7741409
X-RAY DIFFRACTIONf_dihedral_angle_d9.192828
X-RAY DIFFRACTIONf_chiral_restr0.053147
X-RAY DIFFRACTIONf_plane_restr0.004183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8394-2.02450.27621280.23852432X-RAY DIFFRACTION96
2.0245-2.31740.22711340.18212553X-RAY DIFFRACTION100
2.3174-2.91950.21771360.17862587X-RAY DIFFRACTION100
2.9195-39.55910.17521430.152726X-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)
10.12440.0536-0.10510.01460.02780.31840.18890.39920.304-0.2225-0.0851-0.3082-0.4694-0.03520.00160.21890.00210.06780.2170.03570.26176.8218-16.0511-9.3277
20.0742-0.04550.02460.0460.08460.2411-0.0901-0.12010.0535-0.0394-0.0663-0.2388-0.21770.33760.00060.1421-0.0175-0.01950.22640.05270.207611.6173-23.9251.4124
30.1732-0.0089-0.1482-0.0042-0.0070.11570.02070.0925-0.0347-0.0542-0.05110.04490.0387-0.1115-0.00020.15750.02580.01560.1527-0.00480.1552-0.5258-21.8973-6.1634
40.00370.01480.01220.02210.00610.0267-0.0972-0.0616-0.1822-0.07820.1390.13380.6548-0.0551-0.00050.2617-0.00520.02030.27280.06160.2454-14.7072-20.13894.7873
50.2868-0.06240.07450.1952-0.01570.0969-0.1773-0.1182-0.04640.13110.01030.15250.11090.0145-0.00050.22860.04830.02450.1987-0.00420.1636-7.2489-16.99226.9279
60.03450.04050.01710.1586-0.0160.0118-0.2422-0.50280.13260.58370.33850.0116-0.05070.03180.00250.31120.0971-0.00640.3372-0.01290.2183-4.7895-14.206314.232
70.13160.0312-0.21590.0992-0.0610.2330.0047-0.07110.403-0.01040.0219-0.2167-0.13920.1208-00.19660.0093-0.01010.198-0.00620.23611.8365-13.73583.2456
80.0599-0.0922-0.01280.19720.00480.0402-0.1038-0.0584-0.10120.17230.09680.1954-0.0444-0.41550.00010.1531-0.0007-0.00690.21090.01760.1998-0.0921-29.72083.3216
90.2524-0.02810.09340.0773-0.09750.0850.1382-0.0647-0.1322-0.186-0.1285-0.32590.03980.52170.0320.23530.00080.08560.2698-0.02980.26158.474-28.5537-10.9519
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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