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- PDB-2f4a: Triclinic cross-linked lysozyme soaked with thiourea 1.5M -

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Basic information

Entry
Database: PDB / ID: 2f4a
TitleTriclinic cross-linked lysozyme soaked with thiourea 1.5M
ComponentsLysozyme C
KeywordsHYDROLASE / DENATURATION / LYSOZYME / BARNASE / CROSS-LINKED CRYSTALS / GLUTARALDEHYDE / 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
ACETATE ION / NITRATE ION / THIOUREA / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsPrange, T. / Salem, M.
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 23, 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 1.3Aug 23, 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 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)14,8679
Polymers14,3311
Non-polymers5358
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.280, 32.020, 34.310
Angle α, β, γ (deg.)88.53, 108.51, 111.92
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: EGG / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TOU / THIOUREA


Mass: 76.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4N2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 31.9 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: SODIUM NITRATE AS CRYSTALLIZING AGENT CROSS-LINKED BY VAPOR DIFFUSION WITH GLUTARALDEHYDE, PROTIEN CONCENTRATION 20 MG/ML, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 13, 2002 / Details: SI(111) CURVATED MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.949→18.3 Å / Num. all: 7080 / Num. obs: 6985 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4
Reflection shellResolution: 1.949→2.1 Å / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 6.9 / % possible all: 94.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2F2N

2f2n


Resolution: 1.95→10 Å / Num. parameters: 4389 / Num. restraintsaints: 4186 / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rfree0.1607 --
Rwork0.16 --
all-7080 -
obs-6985 96.2 %
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1097
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 32 64 1097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0245
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.066
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0 / Rfactor Rfree error: _ / Num. reflection Rfree: _ / Total num. of bins used: 5

Resolution (Å)Rfactor RworkNum. reflection obs% reflection obs (%)
1.95-2.10.155140691.5
2.1-2.50.148229595.3
2.5-30.142143396.8
3-80.168189598.2
8-100.39752100

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