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- PDB-2f2n: Triclinic hen egg lysozyme cross-linked by glutaraldehyde -

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Basic information

Entry
Database: PDB / ID: 2f2n
TitleTriclinic hen egg lysozyme cross-linked by glutaraldehyde
ComponentsLysozyme C
KeywordsHYDROLASE / denaturation / lysozyme / barnase / cross-linked-crystals / urea / thiourea / bromoethanol
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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.603 Å
AuthorsPrange, T. / Salem, M. / Mauguen, Y.
CitationJournal: Biochim.Biophys.Acta / Year: 2006
Title: On the edge of the denaturation process: Application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations.
Authors: Salem, M. / Mauguen, Y. / Prange, T.
History
DepositionNov 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,7658
Polymers14,3311
Non-polymers4347
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.170, 31.840, 34.220
Angle α, β, γ (deg.)88.67, 108.32, 111.87
Int Tables number1
Space group name H-MP1

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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 / Details: eggs / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.01 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium nitrate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.974 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationMonochromator: SI(III) CURVATED MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.603→8.7 Å / Num. all: 12253 / Num. obs: 12315 / % possible obs: 93.55 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.043 / Net I/σ(I): 32.01
Reflection shellResolution: 1.603→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 17.2 / Rsym value: 0.168 / % possible all: 87.84

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3LZT, 1LKS

3lzt

1lks


Resolution: 1.603→8 Å / Num. parameters: 4727 / Num. restraintsaints: 4203 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 725 -RANDOM
Rwork0.1368 ---
all0.1379 12315 --
obs0.1375 12253 93.9 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 954 / Occupancy sum non hydrogen: 1179
Refinement stepCycle: LAST / Resolution: 1.603→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 28 152 1181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0257
X-RAY DIFFRACTIONs_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.604-1.70.181200.151X-RAY DIFFRACTION187788.3
1.7-1.90.1621900.138X-RAY DIFFRACTION290392.6
2.1-2.50.1491820.129X-RAY DIFFRACTION227695.4
2.5-30.148610.124X-RAY DIFFRACTION141696.5
3-80.173450.14X-RAY DIFFRACTION186598
8-1000.286X-RAY DIFFRACTION5450

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