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- PDB-4wl6: Raster-scanning protein crystallography using micro and nano-focu... -

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Basic information

Entry
Database: PDB / ID: 4wl6
TitleRaster-scanning protein crystallography using micro and nano-focused synchrotron beams
ComponentsLysozyme C
KeywordsHYDROLASE / serial crystallography / crystFEL / Nanopeakcell / nano focused beam / silicone nitride raster scanning
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: 1.85 Å
AuthorsCoquelle, N. / Kapp, U. / Shilova, A. / Weinhausen, B. / Burghammer, M. / Colletier, J.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams.
Authors: Coquelle, N. / Brewster, A.S. / Kapp, U. / Shilova, A. / Weinhausen, B. / Burghammer, M. / Colletier, J.P.
History
DepositionOct 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jul 20, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)16,2932
Polymers16,2581
Non-polymers351
Water36020
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.990, 77.990, 38.510
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-306-

HOH

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Components

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


Mass: 16257.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5 / Details: 50mM Sodium acetate pH 4.5, 16% PEG 4K, 3.5M NaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.832 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.832 Å / Relative weight: 1
ReflectionResolution: 1.85→55.11 Å / Num. obs: 10606 / % possible obs: 100 % / Redundancy: 852.4 % / Net I/σ(I): 8.37
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 643.8 % / Mean I/σ(I) obs: 2.37 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ljn

1ljn


Resolution: 1.85→38.995 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / Phase error: 41.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 536 5.07 %
Rwork0.2282 --
obs0.2304 10577 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→38.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 20 1022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051109
X-RAY DIFFRACTIONf_angle_d0.9011502
X-RAY DIFFRACTIONf_dihedral_angle_d13.138410
X-RAY DIFFRACTIONf_chiral_restr0.035152
X-RAY DIFFRACTIONf_plane_restr0.004203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-2.03620.39751300.31142436X-RAY DIFFRACTION99
2.0362-2.33080.38441380.29082455X-RAY DIFFRACTION100
2.3308-2.93650.32521290.3122502X-RAY DIFFRACTION100
2.9365-39.00360.241390.19852648X-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)
12.7394-0.25713.20320.899-1.43743.9282-0.3270.0841-0.65010.03830.04710.26990.145-0.4827-0.00350.4415-0.01160.1090.35420.04740.481319.2748-8.958723.9255
2-0.07370.3430.0420.8997-0.31612.5338-0.6367-0.1614-0.5230.52680.52990.4165-0.15680.06590.00020.46190.02070.01060.46060.03060.482321.32570.391425.5493
30.189-0.0886-0.0640.0587-0.1180.24610.04050.1813-0.4795-0.6182-0.1594-0.77350.48711.58060.01210.56080.00520.11720.59750.06360.643519.484514.166714.426
40.44840.1418-1.00570.7093-1.20331.0407-0.32750.07870.3319-0.41040.0646-0.2-0.3946-0.24250.00010.70830.06340.02830.6809-0.0070.590416.61446.942511.8341
50.73751.05-0.42442.86090.16770.86890.82281.74471.2009-0.93590.20342.6835-0.7964-1.32730.03930.74030.12530.04980.78530.12480.643413.8744.64255.1196
60.1909-0.90050.07772.0067-1.26020.5655-0.0223-0.10640.0117-0.03440.27340.16890.494-0.35390.00030.6381-0.0201-0.07830.54670.00580.564712.8804-2.180516.1041
70.4290.1822-0.0499-0.14410.2230.2765-0.42790.8741.0522-1.07140.4677-0.3672-1.23881.2606-0.00110.6264-0.06540.07150.6210.01640.591929.4994-0.302115.4074
80.95021.0564-1.23680.5568-1.05670.7579-0.7409-0.6764-1.5067-0.1590.134-1.31970.9065-0.0482-0.02290.62130.04310.06720.71790.2360.644427.5329-9.604630.9588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 50 )
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 98 )
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 114 )
8X-RAY DIFFRACTION8chain 'A' and (resid 115 through 129 )

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