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- PDB-4n5r: Hen egg-white lysozyme phased using free-electron laser data -

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Basic information

Entry
Database: PDB / ID: 4n5r
TitleHen egg-white lysozyme phased using free-electron laser data
ComponentsLysozyme C
KeywordsHYDROLASE / free-electron laser
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
Chem-DO3 / GADOLINIUM ATOM / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBarends, T.R.M. / Foucar, L. / Botha, S. / Doak, R.B. / Shoeman, R.L. / Nass, K. / Koglin, J.E. / Williams, G.J. / Boutet, S. / Messerschmidt, M. / Schlichting, I.
CitationJournal: Nature / Year: 2014
Title: De novo protein crystal structure determination from X-ray free-electron laser data.
Authors: Barends, T.R. / Foucar, L. / Botha, S. / Doak, R.B. / Shoeman, R.L. / Nass, K. / Koglin, J.E. / Williams, G.J. / Boutet, S. / Messerschmidt, M. / Schlichting, I.
History
DepositionOct 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 1.3Jan 22, 2014Group: Database references
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4555
Polymers14,3311
Non-polymers1,1234
Water93752
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, 39.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32N4O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 59667

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: batch / pH: 3
Details: 20 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0, stored in 8% NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in storage solution + 100 mM gadoteridol, batch, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.45 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Mar 8, 2013
RadiationMonochromator: FREE-ELECTRON LASER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 7294 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
DAQdata collection
PHASERphasing
REFMAC5.5.0110refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VDS

1vds


Resolution: 2.1→39.55 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.243 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25632 385 5 %RANDOM
Rwork0.23098 ---
obs0.2322 7294 99.99 %-
all-7287 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0 Å2
2---0.27 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 58 52 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191072
X-RAY DIFFRACTIONr_bond_other_d0.0010.02989
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9521448
X-RAY DIFFRACTIONr_angle_other_deg0.8413.0072245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6632350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04315164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2291511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4351.5629
X-RAY DIFFRACTIONr_mcbond_other0.081.5265
X-RAY DIFFRACTIONr_mcangle_it0.8622998
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3473443
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2244.5450
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 31 -
Rwork0.297 523 -
obs--100 %

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