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- PDB-3lzt: REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 3lzt
TitleREFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION
ComponentsLYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / GLYCOSIDASE
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 / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.925 Å
AuthorsWalsh, M.A. / Schneider, T. / Sieker, L.C. / Dauter, Z. / Lamzin, V. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Refinement of triclinic hen egg-white lysozyme at atomic resolution.
Authors: Walsh, M.A. / Schneider, T.R. / Sieker, L.C. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Refinement of Triclinic Lysozyme: I. Fourier and Least-Squares Methods
Authors: Hodsdon, J.M. / Brown, G.M. / Sieker, L.C. / Jensen, L.H.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Refinement of Triclinic Lysozyme: II. The Method of Stereochemically Restrained Least Squares
Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H.
History
DepositionMar 23, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / refine / reflns / reflns_shell / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model / _reflns.d_resolution_high / _reflns_shell.d_res_high / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,88010
Polymers14,3311
Non-polymers5499
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.650, 30.800, 33.630
Angle α, β, γ (deg.)88.30, 107.40, 112.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NITRATE AND ACETATE IONS PRESENT / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 1.69 Å3/Da / Density % sol: 26.9 %
Crystal growMethod: batch method / pH: 4.6
Details: BATCH METHOD USED. 1% PROTEIN SOLUTION IN 100MM SODIUM ACETATE PH 4.5-4.6. SODIUM NITRATE ADDED TO A CONCENTRATION OF 20MGS/ML. CRYSTALS GROWN AT ROOM TEMPERATURE., batch method
PH range: 4.5-4.6 / Temp details: room temp
Crystal grow
*PLUS
Temperature: 296 K / pH: 4.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein solution11
2100 mMsodium acetate11
32 %(w/v)sodium nitrate12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: SEGMENTED MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 0.925→25 Å / Num. obs: 58373 / % possible obs: 90.1 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 29.1
Reflection shellResolution: 0.925→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
Num. measured all: 232156
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building
SHELXL-96refinement
SHELXL-96phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.925→20 Å / Num. parameters: 12844 / Num. restraintsaints: 16207 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: WATER OCCUPANCIES REFINED. TWO SECTIONS OF THE MAIN CHAIN MODELED IN TWO DISCRETE CONFORMATIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.1136 1776 3 %
all0.0925 58367 -
obs0.093 -90.1 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 28 / Occupancy sum hydrogen: 923.71 / Occupancy sum non hydrogen: 1230.1
Refinement stepCycle: LAST / Resolution: 0.925→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 44 250 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.044
X-RAY DIFFRACTIONs_similar_dist0.025
X-RAY DIFFRACTIONs_from_restr_planes0.426
X-RAY DIFFRACTIONs_zero_chiral_vol0.156
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.173
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.029
X-RAY DIFFRACTIONs_approx_iso_adps0.087
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.093
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg36.84
X-RAY DIFFRACTIONs_planar_d0.050.051
X-RAY DIFFRACTIONs_plane_restr0.020.03
X-RAY DIFFRACTIONs_chiral_restr0.150.25

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