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- PDB-3rz4: Hen egg-white lysozyme in HEPES buffer at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 3rz4
TitleHen egg-white lysozyme in HEPES buffer at pH 7.5
ComponentsLysozyme C
KeywordsHYDROLASE
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: 1.8 Å
AuthorsPeretoltchine, K. / Bryson, S. / Pai, E.F.
CitationJournal: To be Published
Title: Hen egg-white lysozyme in HEPES buffer at pH 7.5
Authors: Peretoltchine, K. / Bryson, S. / Pai, E.F.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)14,5692
Polymers14,3311
Non-polymers2381
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.200, 77.200, 36.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-180-

HOH

21A-221-

HOH

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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 / Fragment: unp residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M potassium sodium tartrate tetrahydrate, 0.1M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2011
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→17 Å / Num. all: 10803 / Num. obs: 10731 / % possible obs: 97 % / Redundancy: 6.5 % / Rsym value: 0.099 / Net I/σ(I): 31.6
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.8-1.853.784.450.099186.7
1.85-1.95.797.12194.9
1.9-1.956.739.45198.4
1.95-26.7311.94195.6
2-2.056.9813.941100
2.05-2.156.8917.23197.9
2.15-2.256.9120.84198.1
2.25-2.356.8924.7199
2.35-2.5727.28199.5
2.5-2.65732.1199.1
2.65-2.856.9938.65199.4
2.85-3.16.9245.66199.7
3.1-3.456.9256.96199.7
3.45-46.9269.461100
4-5.156.7477.41100
5.156.181.86198.9

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3FE0

3fe0


Resolution: 1.8→17 Å / σ(F): 40 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 523 -random
Rwork0.2083 ---
all-10731 --
obs-10538 98.2 %-
Displacement parametersBiso mean: 25.3829 Å2
Baniso -1Baniso -2Baniso -3
1--1.146 Å20 Å2-0 Å2
2---1.146 Å2-0 Å2
3---2.291 Å2
Refinement stepCycle: LAST / Resolution: 1.8→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 15 115 1131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.001
X-RAY DIFFRACTIONc_scbond_it1.502
X-RAY DIFFRACTIONc_mcangle_it1.527
X-RAY DIFFRACTIONc_scangle_it2.321

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