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- PDB-1wtn: The structure of HEW Lysozyme Orthorhombic Crystal Growth under a... -

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Basic information

Entry
Database: PDB / ID: 1wtn
TitleThe structure of HEW Lysozyme Orthorhombic Crystal Growth under a High Magnetic Field
ComponentsLysozyme C
KeywordsHYDROLASE / Allergen
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: 1.13 Å
AuthorsSaijo, S. / Yamada, Y. / Sato, T. / Tanaka, N. / Matsui, T. / Sazaki, G. / Nakajima, K. / Matsuura, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and ...Title: Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity.
Authors: Saijo, S. / Yamada, Y. / Sato, T. / Tanaka, N. / Matsui, T. / Sazaki, G. / Nakajima, K. / Matsuura, Y.
History
DepositionNov 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.540, 73.830, 30.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: egg / Cellular location: cytoplasm(white) / 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.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 313 K / Method: under a high magnetic field of 10t / pH: 4.5
Details: NaCl, sodium acetate, pH 4.5, under a High Magnetic Field of 10T, temperature 313K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12961
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B11
SYNCHROTRONPhoton Factory BL-18B21
Detector
TypeIDDetectorDate
WEISSENBERG1DIFFRACTOMETERJun 21, 1999
CUSTOM-MADE2DIFFRACTOMETEROct 20, 1999
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. all: 34622 / Num. obs: 34449 / % possible obs: 99.5 % / Observed criterion σ(I): 3
Reflection shellResolution: 1.13→1.16 Å / % possible all: 71.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→16 Å / σ(F): 3
Details: technically defined here as 10 T and 0 T crystals, were grown by exposing them to a high magnetic field of 10 T (this entry 1WTN) and a control geomagnetic field of 40 uT(entry 1WTM), ...Details: technically defined here as 10 T and 0 T crystals, were grown by exposing them to a high magnetic field of 10 T (this entry 1WTN) and a control geomagnetic field of 40 uT(entry 1WTM), respectively (Sato,T., Yamada,Y., Saijo,S., Hori,T., Hirose,R., Tanaka,N., Sazaki,G., Nakajima,K., Igarashi,N., Tanaka,M. & Matsuura,Y. (2000). Acta Cryst. D56, 1079-1083.). A continuous homogeneous magnetic field of 10 T was produced by a liquid helium-free superconducting magnet (JMTD-10T100M9) (Japan Magnetic Technology Inc., Tokyo, Japan). Orthorhombic lysozyme crystals were grown, in the high magnetic field, via the batch crystallization method. The crystal growth conditions were 250 mg.ml-1 lysozyme, 42 mM NaCl in 50 mM sodium acetate buffer with pH 4.5 at 313 K; 11 days duration. The dimensions of the 10 T and 0 T crystals were typically 0.45 X 0.50 X 2.00 and 0.50 X 0.50 X 2.00 mm, respectively. The starting model for molecular replacement in each case was the refined atomic coordinates (entry 1BGI) of the HEW lysozyme obtained from the PDB (Oki,H., Matsuura,Y., Komatsu,H. & Chernov,A.A. (1999). Acta Cryst. D55, 114- 121.), i.e., our best resolution structure for the orthorhombic lysozyme refined so far (at 1.7 A resolution).
RfactorNum. reflection
Rfree0.2 -
Rwork0.17 -
obs-34449
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.13→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 1 116 1126
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d0.018

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