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- PDB-4axt: CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME FROM AN AUTO HARVESTE... -

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Basic information

Entry
Database: PDB / ID: 4axt
TitleCRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME FROM AN AUTO HARVESTED CRYSTAL, Control Experiment
ComponentsLYSOZYME C
KeywordsHYDROLASE / AUTOMATION / HIGH-THROUGHPUT CRYSTALLIZATION / CRYSTAL MOUNTING / CRYSTALLIZATION MICROPLATES
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
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCipriani, F. / Rower, M. / Landret, C. / Zander, U. / Felisaz, F. / Marquez, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Crystal Direct: A New Method for Automated Crystal Harvesting Based on Laser-Induced Photoablation of Thin Films
Authors: Cipriani, F. / Rower, M. / Landret, C. / Zander, U. / Felisaz, F. / Marquez, J.A.
History
DepositionJun 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Atomic model / Other
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.242, 78.242, 37.473
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-2104-

HOH

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Components

#1: Protein LYSOZYME C / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D IV / GAL D 4


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.53 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.1→37.48 Å / Num. obs: 47356 / % possible obs: 99.3 % / Observed criterion σ(I): 3.1 / Redundancy: 12.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.1 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.1→27.66 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.842 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17719 2388 5 %RANDOM
Rwork0.16133 ---
obs0.1621 44908 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.1→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 156 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191036
X-RAY DIFFRACTIONr_bond_other_d0.0020.02716
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9031404
X-RAY DIFFRACTIONr_angle_other_deg2.5643.0091711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51723.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18315172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7271511
X-RAY DIFFRACTIONr_chiral_restr0.2540.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021176
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02236
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr10.64931036
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded15.72551012
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 140 -
Rwork0.2 2879 -
obs--93.29 %

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