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- PDB-3m3u: Effect of temperature on tryptophan fluorescence in lysozyme crystals -

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Basic information

Entry
Database: PDB / ID: 3m3u
TitleEffect of temperature on tryptophan fluorescence in lysozyme crystals
ComponentsLysozyme C
KeywordsHYDROLASE / Hen egg white lysozyme / Tryptophan fluorescence / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond / Glycosidase
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: 2.35 Å
AuthorsVarshney, N.K. / Sitaramam, V.
Citation
Journal: TO BE PUBLISHED
Title: Effect of temperature on tryptophan fluorescence in lysozyme crystals
Authors: Varshney, N.K. / Sitaramam, V.
#1: 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
DepositionMar 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3903
Polymers14,3311
Non-polymers582
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.095, 79.095, 38.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Sodium Acetate, 7% NaCl, 25% Ethylene glycol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.514 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 16, 2005 / Details: Mirrors
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.35→19.77 Å / Num. all: 5388 / Num. obs: 5384 / % possible obs: 99.93 % / Observed criterion σ(F): 1 / Redundancy: 12.86 % / Biso Wilson estimate: 35.74 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.26
Reflection shellResolution: 2.349→2.409 Å / Redundancy: 10.43 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5.211 / Num. unique all: 363 / % possible all: 99.21

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BVX

1bvx


Resolution: 2.35→19.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.424 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19924 245 4.6 %RANDOM
Rwork0.1658 ---
all0.177 5379 --
obs0.16742 5139 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.524 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 64 1067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211012
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9041371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87623.40447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93215160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.668159
X-RAY DIFFRACTIONr_chiral_restr0.110.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02780
X-RAY DIFFRACTIONr_mcbond_it0.9921.5634
X-RAY DIFFRACTIONr_mcangle_it1.95821005
X-RAY DIFFRACTIONr_scbond_it3.1933378
X-RAY DIFFRACTIONr_scangle_it5.2814.5366
LS refinement shellResolution: 2.349→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 16 -
Rwork0.177 363 -
obs-363 99.21 %

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