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- PDB-5oer: Hen egg-white lysozyme refined against 5000 9 keV diffraction patterns -

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Basic information

Entry
Database: PDB / ID: 5oer
TitleHen egg-white lysozyme refined against 5000 9 keV diffraction patterns
ComponentsLysozyme C
KeywordsHYDROLASE / Free-electron laser / experimental phasing / multiwavelength anomalous dispersion
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
Chem-DO3 / GADOLINIUM ATOM / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 1.9 Å
AuthorsGorel, A. / Schlichting, I.
CitationJournal: Nat Commun / Year: 2017
Title: Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability.
Authors: Gorel, A. / Motomura, K. / Fukuzawa, H. / Doak, R.B. / Grunbein, M.L. / Hilpert, M. / Inoue, I. / Kloos, M. / Kovacsova, G. / Nango, E. / Nass, K. / Roome, C.M. / Shoeman, R.L. / Tanaka, R. ...Authors: Gorel, A. / Motomura, K. / Fukuzawa, H. / Doak, R.B. / Grunbein, M.L. / Hilpert, M. / Inoue, I. / Kloos, M. / Kovacsova, G. / Nango, E. / Nass, K. / Roome, C.M. / Shoeman, R.L. / Tanaka, R. / Tono, K. / Joti, Y. / Yabashi, M. / Iwata, S. / Foucar, L. / Ueda, K. / Barends, T.R.M. / Schlichting, I.
History
DepositionJul 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.5Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,4786
Polymers14,3311
Non-polymers1,1465
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-30 kcal/mol
Surface area7010 Å2
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-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
#3: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: batch mode / Details: Sodium chloride

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.38 Å
DetectorType: MPCCD / Detector: CCD / Date: Jan 1, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.9→57 Å / Num. obs: 10028 / % possible obs: 100 % / Redundancy: 68 % / CC1/2: 0.876 / R split: 0.248 / Net I/σ(I): 4.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 48 % / CC1/2: 0.867 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→55.93 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.894 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21435 477 4.6 %RANDOM
Rwork0.18566 ---
obs0.18698 9795 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.675 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.9→55.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 59 70 1121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191090
X-RAY DIFFRACTIONr_bond_other_d0.0010.02995
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.951476
X-RAY DIFFRACTIONr_angle_other_deg0.94632278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29223.26952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35715166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9541511
X-RAY DIFFRACTIONr_chiral_restr0.1760.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
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_it0.5361.555521
X-RAY DIFFRACTIONr_mcbond_other0.5361.553520
X-RAY DIFFRACTIONr_mcangle_it0.9282.329653
X-RAY DIFFRACTIONr_mcangle_other0.9282.332654
X-RAY DIFFRACTIONr_scbond_it0.6711.696569
X-RAY DIFFRACTIONr_scbond_other0.6711.696567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1612.495823
X-RAY DIFFRACTIONr_long_range_B_refined3.53713.11306
X-RAY DIFFRACTIONr_long_range_B_other3.3812.951284
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 40 -
Rwork0.199 706 -
obs--100 %

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