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- PDB-2d4i: Monoclinic hen egg-white lysozyme crystallized at pH4.5 form heav... -

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Basic information

Entry
Database: PDB / ID: 2d4i
TitleMonoclinic hen egg-white lysozyme crystallized at pH4.5 form heavy water solution
ComponentsLysozyme C
KeywordsHYDROLASE / phase transition / rigid-body motion / TLS analysis
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
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 1.4Oct 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_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9958
Polymers28,6622
Non-polymers3336
Water4,216234
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3932
Polymers14,3311
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6026
Polymers14,3311
Non-polymers2715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.008, 62.915, 60.494
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: D2O

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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: 1.81 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 298 K / Method: batch method / pH: 4.5
Details: 1% protein, 2% sodium nitrate, D2O solution with pD 4.5 adjusted with 1M acetic acid, batch method, temperature 298K

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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: May 7, 2004 / Details: Conforcal 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: 1.13→17.2 Å / Num. all: 77767 / Num. obs: 68963 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.39 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.13→1.17 Å / Rmerge(I) obs: 0.415 / % possible all: 57.3

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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 1LJ4

1lj4


Resolution: 1.16→17.2 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
Rfree0.175 3314 random
Rwork0.136 --
obs0.137 66282 -
Refinement stepCycle: LAST / Resolution: 1.16→17.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 21 234 2257
LS refinement shellResolution: 1.13→1.22 Å / Rfactor Rwork: 0.376

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