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- PDB-4lzt: ATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K -

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Basic information

Entry
Database: PDB / ID: 4lzt
TitleATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K
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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / STRUCTURE KNOWN / Resolution: 0.95 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 31, 1997Processing site: BNL
Revision 1.0Apr 1, 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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)14,7037
Polymers14,3311
Non-polymers3726
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.240, 31.870, 34.230
Angle α, β, γ (deg.)88.52, 108.53, 111.89
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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 31.8 %
Crystal growMethod: batch method / pH: 4.5
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
*PLUS
Crystal grow
*PLUS
Temperature: 296 K / 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: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.862
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.862 Å / Relative weight: 1
ReflectionResolution: 0.95→21 Å / Num. obs: 61265 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.273 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 289540
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building
SHELXL-96refinement
SHELXL-96phasing
RefinementMethod to determine structure: STRUCTURE KNOWN
Starting model: PDB ENTRY 2LZT

2lzt


Resolution: 0.95→21 Å / Num. parameters: 10801 / Num. restraintsaints: 13288 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
Details: WATER OCCUPANCIES REFINED DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.147 1870 3 %RANDOM
all0.1082 61258 --
obs0.1144 -96.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 920.89 / Occupancy sum non hydrogen: 1123.7
Refinement stepCycle: LAST / Resolution: 0.95→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 24 139 1183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes0.39
X-RAY DIFFRACTIONs_zero_chiral_vol0.128
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.152
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.044
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.071
X-RAY DIFFRACTIONs_approx_iso_adps0.095
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.147 / Rfactor Rwork: 0.1144
Solvent computation
*PLUS
Displacement parameters
*PLUS

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