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- PDB-2d4j: Transformed monoclinic crystal of hen egg-white lysozyme from a h... -

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Basic information

Entry
Database: PDB / ID: 2d4j
TitleTransformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution
ComponentsLysozyme C
KeywordsHYDROLASE / phase transition / rigid-body motion / TLS analysis
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
DEUTERATED WATER / NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsHarata, K. / Akiba, T.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Structural phase transition of monoclinic crystals of hen egg-white lysozyme
Authors: Harata, K. / Akiba, T.
History
DepositionOct 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,5795
Polymers14,3311
Non-polymers2484
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.460, 58.180, 30.850
Angle α, β, γ (deg.)90.00, 111.33, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a molecule in the asymmetric unit.

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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) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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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: 1.54 Å3/Da / Density % sol: 20.31 %
Crystal growTemperature: 293 K / Method: phase transition / pH: 4.5
Details: The crystal was created by the dehydration-induced phase transition of a monoclinic crystal obtained from a heavy water solution at pD 4.5, temperature 293K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 30, 2004 / Details: Confocal Max-Flux optics
RadiationMonochromator: curved mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.16→12.3 Å / Num. all: 30199 / Num. obs: 25242 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.09 % / Rmerge(I) obs: 0.106
Reflection shellResolution: 1.16→1.2 Å / Rmerge(I) obs: 0.299 / % possible all: 52.8

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Processing

Software
NameVersionClassification
SaintPLusdata reduction
X-PLORmodel building
SHELXL-97refinement
SMARTV. 6000data reduction
SAINTPLUSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XEK

1xek


Resolution: 1.16→12.3 Å / σ(F): 0 / Stereochemistry target values: SHELX97 default
Details: The author asigned the Rfree reflections by the following SHELXL97 input command line L.S. 5 -20 which indicates 5 cycles of least-squares calculation and ignore every 20th reflections (5%) ...Details: The author asigned the Rfree reflections by the following SHELXL97 input command line L.S. 5 -20 which indicates 5 cycles of least-squares calculation and ignore every 20th reflections (5%) in the refinement for the Rfree calculation
RfactorNum. reflectionSelection details
Rfree0.133 1261 Random
Rwork0.097 --
obs0.098 25218 -
Refinement stepCycle: LAST / Resolution: 1.16→12.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 16 129 1146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.096
LS refinement shellResolution: 1.16→1.22 Å / Rfactor Rwork: 0.169

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