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- PDB-1lz8: LYSOZYME PHASED ON ANOMALOUS SIGNAL OF SULFURS AND CHLORINES -

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Basic information

Entry
Database: PDB / ID: 1lz8
TitleLYSOZYME PHASED ON ANOMALOUS SIGNAL OF SULFURS AND CHLORINES
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / O-GLYCOSYL / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsDauter, Z. / Dauter, M. / De La Fortelle, E. / Bricogne, G. / Sheldrick, G.M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Can anomalous signal of sulfur become a tool for solving protein crystal structures?
Authors: Dauter, Z. / Dauter, M. / de La Fortelle, E. / Bricogne, G. / Sheldrick, G.M.
History
DepositionMar 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,63810
Polymers14,3311
Non-polymers3079
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.810, 78.810, 36.800
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 PROTEIN (LYSOZYME)


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 8 CHLORIDE AND 1 SODIUM ION PRESENT / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.6
Details: BATCH METHOD. 20 MG/ML PROTEIN SOLUTION IN 50MM SODIUM ACETATE PH 4.6 AND 10% NACL. CRYSTALS GROWN AT ROOM TEMPERATURE.
Crystal
*PLUS
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
210 %(w/v)11NaCl

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.927
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: SEGMENTED MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 0.92→25 Å / Num. obs: 58373 / % possible obs: 90.1 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 29.1
Reflection shellResolution: 0.93→0.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.17 / % possible all: 78
Reflection
*PLUS
Highest resolution: 1.53 Å / Lowest resolution: 60 Å / % possible obs: 100 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 1.53 Å / Lowest resolution: 1.56 Å / % possible obs: 100 % / Rmerge(I) obs: 0.19

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8LYZ

8lyz


Resolution: 1.53→25 Å / SU B: 1.753 / SU ML: 0.067 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.31 915 5 %RANDOM
Rwork0.22 ---
obs0.22 17923 100 %-
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.043 Å20 Å20 Å2
2--1.043 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.53→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 9 224 1234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.02
X-RAY DIFFRACTIONp_angle_d0.0440.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.23
X-RAY DIFFRACTIONp_mcangle_it2.95
X-RAY DIFFRACTIONp_scbond_it4.36
X-RAY DIFFRACTIONp_scangle_it5.18
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.180.15
X-RAY DIFFRACTIONp_singtor_nbd0.1680.3
X-RAY DIFFRACTIONp_multtor_nbd0.2940.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.210.3
X-RAY DIFFRACTIONp_planar_tor5.77
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.150.18

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