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- PDB-1lz9: ANOMALOUS SIGNAL OF SOLVENT BROMINES USED FOR PHASING OF LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1lz9
TitleANOMALOUS SIGNAL OF SOLVENT BROMINES USED FOR PHASING OF LYSOZYME
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / LYSOZYME / SOLVENT BROMIDES / ANOMALOUS DISPERSION / SINGLE WAVELENGTH
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
BROMIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDauter, Z. / Dauter, M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Anomalous signal of solvent bromides used for phasing of lysozyme.
Authors: Dauter, Z. / Dauter, M.
History
DepositionMar 15, 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
Revision 1.4Nov 6, 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: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8348
Polymers14,3311
Non-polymers5027
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.600, 78.600, 37.200
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: BROMIDE AND SODIUM IONS PRESENT / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.6
Details: CRYSTALLIZED IN HANGING DROPS. 15 MG/ML PROTEIN SOLUTION IN 100 MM SODIUM ACETATE PH 4.6 AND 1 M SODIUM BROMIDE.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.5 M1dropNaBr
30.1 Msodium acetate1drop
41 M1reservoirNaBr
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9188, 0.9195, 0.9198, 0.9201
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: BENT MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91881
20.91951
30.91981
40.92011
ReflectionResolution: 1.7→20 Å / Num. obs: 13429 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 50.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 10 / Rsym value: 0.182 / % possible all: 80

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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: 1.7→20 Å / SU B: 2.7 / SU ML: 0.094 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1318 10 %RANDOM 10 %
Rwork0.21 ---
obs0.21 13309 99 %-
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.644 Å20 Å20 Å2
2--0.644 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 0 7 197 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0320.02
X-RAY DIFFRACTIONp_angle_d0.0530.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.113
X-RAY DIFFRACTIONp_mcangle_it3.695
X-RAY DIFFRACTIONp_scbond_it5.716
X-RAY DIFFRACTIONp_scangle_it6.868
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.2640.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2990.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2540.3
X-RAY DIFFRACTIONp_planar_tor6.67
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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