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- PDB-4etb: lysozyme, room temperature, 200 kGy dose -

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Basic information

Entry
Database: PDB / ID: 4etb
Titlelysozyme, room temperature, 200 kGy dose
ComponentsLysozyme C
KeywordsHYDROLASE / 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
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 / FOURIER SYNTHESIS / Resolution: 1.908 Å
AuthorsBoutet, S. / Lomb, L. / Williams, G. / Barends, T. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D. / Steinbrener, J. / Shoeman, R. ...Boutet, S. / Lomb, L. / Williams, G. / Barends, T. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D. / Steinbrener, J. / Shoeman, R. / Messerschmidt, M. / Barty, A. / White, T. / Kassemeyer, S. / Kirian, R. / Seibert, M. / Montanez, P. / Kenney, C. / Herbst, R. / Hart, P. / Pines, J. / Haller, G. / Gruner, S. / Philllip, H. / Tate, M. / Hromalik, M. / Koerner, L. / van Bakel, N. / Morse, J. / Ghonsalves, W. / Arnlund, D. / Bogan, M. / Calemann, C. / Fromme, R. / Hampton, C. / Hunter, M. / Johansson, L. / Katona, G. / Kupitz, C. / Liang, M. / Martin, A. / Nass, K. / Redecke, L. / Stellato, F. / Timneanu, N. / Wang, D. / Zatsepin, N. / Schafer, D. / Defever, K. / Neutze, R. / Fromme, P. / Spence, J. / Chapman, H. / Schlichting, I.
CitationJournal: Science / Year: 2012
Title: High-resolution protein structure determination by serial femtosecond crystallography.
Authors: Boutet, S. / Lomb, L. / Williams, G.J. / Barends, T.R. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D.P. / Steinbrener, J. / Shoeman, R.L. / Messerschmidt, M. / Barty, A. / White, T. ...Authors: Boutet, S. / Lomb, L. / Williams, G.J. / Barends, T.R. / Aquila, A. / Doak, R.B. / Weierstall, U. / DePonte, D.P. / Steinbrener, J. / Shoeman, R.L. / Messerschmidt, M. / Barty, A. / White, T.A. / Kassemeyer, S. / Kirian, R.A. / Seibert, M.M. / Montanez, P.A. / Kenney, C. / Herbst, R. / Hart, P. / Pines, J. / Haller, G. / Gruner, S.M. / Philipp, H.T. / Tate, M.W. / Hromalik, M. / Koerner, L.J. / van Bakel, N. / Morse, J. / Ghonsalves, W. / Arnlund, D. / Bogan, M.J. / Caleman, C. / Fromme, R. / Hampton, C.Y. / Hunter, M.S. / Johansson, L.C. / Katona, G. / Kupitz, C. / Liang, M. / Martin, A.V. / Nass, K. / Redecke, L. / Stellato, F. / Timneanu, N. / Wang, D. / Zatsepin, N.A. / Schafer, D. / Defever, J. / Neutze, R. / Fromme, P. / Spence, J.C. / Chapman, H.N. / Schlichting, I.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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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)14,3672
Polymers14,3311
Non-polymers351
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 79.300, 38.200
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-373-

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-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: grown in Linbro plates in hanging or sitting drop geometry. Drops of equal volume of protein (20 mg/ml) and reservoir solution (1 M NaAc pH 3.0, 9-10 % NaCl, 6 % PEG 6000) were mixed. For ...Details: grown in Linbro plates in hanging or sitting drop geometry. Drops of equal volume of protein (20 mg/ml) and reservoir solution (1 M NaAc pH 3.0, 9-10 % NaCl, 6 % PEG 6000) were mixed. For the measurements, the crystals were equilibrated in 1 M NaAc pH 3.4, 10 % NaCl, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2011
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→36 Å / Num. all: 10041 / Num. obs: 10041 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.908→35.464 Å / SU ML: 0.29 / σ(F): 2.01 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 505 5.1 %RANDOM
Rwork0.1653 ---
obs0.1666 9910 99.76 %-
all-9910 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.125 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8047 Å2-0 Å20 Å2
2---0.8047 Å20 Å2
3---1.6094 Å2
Refinement stepCycle: LAST / Resolution: 1.908→35.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 73 1075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061025
X-RAY DIFFRACTIONf_angle_d1.0471381
X-RAY DIFFRACTIONf_dihedral_angle_d13.648365
X-RAY DIFFRACTIONf_chiral_restr0.079144
X-RAY DIFFRACTIONf_plane_restr0.003181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.908-2.09950.19181270.15322263X-RAY DIFFRACTION99
2.0995-2.40330.19131220.15132323X-RAY DIFFRACTION100
2.4033-3.02760.20411280.17752339X-RAY DIFFRACTION100
3.0276-35.47020.18031280.16792480X-RAY DIFFRACTION100

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