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- PDB-1c10: CRYSTAL STRUCTURE OF HEW LYSOZYME UNDER PRESSURE OF XENON (8 BAR) -

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Basic information

Entry
Database: PDB / ID: 1c10
TitleCRYSTAL STRUCTURE OF HEW LYSOZYME UNDER PRESSURE OF XENON (8 BAR)
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / HYDROPHOBIC CAVITY / XENON COMPLEX
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 / OTHER / Resolution: 2.03 Å
AuthorsPrange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R.
Citation
Journal: Proteins / Year: 1998
Title: Exploring hydrophobic sites in proteins with xenon or krypton.
Authors: Prange, T. / Schiltz, M. / Pernot, L. / Colloc'h, N. / Longhi, S. / Bourguet, W. / Fourme, R.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1995
Title: The Influence of Temperature on Lysozyme Crystals. Structure and Dynamics of Protein and Water
Authors: Kurinov, I.V. / Harrison, R.W.
History
DepositionJul 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,96111
Polymers14,3311
Non-polymers63010
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.530, 78.530, 37.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-150-

XE

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Components

#1: Protein PROTEIN (LYSOZYME)


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: EGG WHITE / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsOCCUPANCY FACTORS WERE REFINED. THE FIRST SITE IS ON A SPECIAL POSSITION AND HENCE REAL OCCUPANCY ...OCCUPANCY FACTORS WERE REFINED. THE FIRST SITE IS ON A SPECIAL POSSITION AND HENCE REAL OCCUPANCY IS TWICE THE REFINED VALUE

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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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growpH: 5.5 / Details: SODIUM CHLORIDE, PH = 5.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %elastase11
20.01 Msodium acetate11
30.02 Msodium sulfate11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.961
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 1996 / Details: MULTILAYER MIRROR
RadiationMonochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 2.03→9.9 Å / Num. obs: 6454 / % possible obs: 79 % / Observed criterion σ(I): 4 / Redundancy: 5.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 8.9
Reflection shellResolution: 2.03→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.3 / % possible all: 59
Reflection shell
*PLUS
% possible obs: 59 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
SHELXL-97refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1LSE

1lse


Resolution: 2.03→9.9 Å / Num. parameters: 4285 / Num. restraintsaints: 4086 / σ(F): 4 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE
RfactorNum. reflection% reflectionSelection details
all0.172 6454 --
obs0.17 -76.7 %-
Rfree--0.218 %RANDOM
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2.03→9.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 10 69 1080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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