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- PDB-1xek: THE CRYSTAL STRUCTURES OF LYSOZYME AT VERY LOW LEVELS OF HYDRATION -

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Basic information

Entry
Database: PDB / ID: 1xek
TitleTHE CRYSTAL STRUCTURES OF LYSOZYME AT VERY LOW LEVELS OF HYDRATION
ComponentsLYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / ENZYME MONOCLINIC 5% R.H. FORM
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNagendra, H.G. / Sukumar, N. / Vijayan, M.
Citation
Journal: Proteins / Year: 1998
Title: Role of water in plasticity, stability, and action of proteins: the crystal structures of lysozyme at very low levels of hydration.
Authors: Nagendra, H.G. / Sukumar, N. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Characterization of Lysozyme Crystals with Unusually Low Solvent Content
Authors: Nagendra, H.G. / Sudarsanakumar, C. / Vijayan, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content
Authors: Madhusudan / Kodandapani, R. / Vijayan, M.
#3: Journal: J.Appl.Crystallogr. / Year: 1993
Title: Comparison of Radiation Induced Decay and Structure Refinement from X-Ray Data Collected from Lysozyme Crystals at Low and Ambient Temperatures
Authors: Young, A.C.M. / Dewan, J.C. / Nave, C. / Tilton, R.F.
#4: Journal: J.Biol.Chem. / Year: 1990
Title: Crystal Structure of Low Humidity Tetragonal Lysozyme at 2.1-A Resolution. Variability in Hydration Shell and its Structural Consequences
Authors: Kodandapani, R. / Suresh, C.G. / Vijayan, M.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 26, 2016Group: Other
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.318, 54.729, 30.681
Angle α, β, γ (deg.)90.00, 111.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LYSOZYME / / HEN (GALLUS GALLUS) EGG-WHITE LYSOZYME / MUCOPEPTIDE / N-ACETYLMURAMYL HYDROLASE


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.38 Å3/Da / Density % sol: 11.08 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 3, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 3175 / % possible obs: 86.02 % / Redundancy: 1.87 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 29.55
Reflection shellResolution: 2.265→2.362 Å / Redundancy: 1.13 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.146 / % possible all: 32.4
Reflection
*PLUS
Num. measured all: 5932

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 88% LOW HUMIDITY STRUCTURE

Resolution: 2.3→10 Å / Cross valid method: A POSTERIORI / σ(F): 4 / Details: X-PLOR WAS ALSO USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.304 --RANDOM
Rwork0.197 ---
obs-2705 73.29 %-
Displacement parametersBiso mean: 29.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 46 1047
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1031
X-RAY DIFFRACTIONp_mcangle_it1.911.5
X-RAY DIFFRACTIONp_scbond_it3.91
X-RAY DIFFRACTIONp_scangle_it4.71.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1250.12
X-RAY DIFFRACTIONp_singtor_nbd0.2390.5
X-RAY DIFFRACTIONp_multtor_nbd0.370.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2870.5
X-RAY DIFFRACTIONp_planar_tor2.55
X-RAY DIFFRACTIONp_staggered_tor26.320
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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