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- PDB-2hu3: Parent Structure of Hen Egg White Lysozyme grown in acidic pH 4.8... -

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Basic information

Entry
Database: PDB / ID: 2hu3
TitleParent Structure of Hen Egg White Lysozyme grown in acidic pH 4.8. Refinement for comparison with crosslinked molecules of lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / tetragonal / Hen egg-white lysozyme / acidic pH 4.8
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
AMMONIUM ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsFrolow, F. / Lagziel-Simis, S. / Cohen-Hadar, N. / Wine, Y. / Freeman, A.
CitationJournal: To be Published
Title: Monitoring influence of pH on the molecular and crystal structure of hen egg-white tetragonal lysozyme
Authors: Lagziel-Simis, S. / Wine, Y. / Cohen-Hadar, N. / Freeman, A. / Frolow, F.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: 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.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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,21825
Polymers14,3311
Non-polymers88724
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Lysozyme C
hetero molecules

A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,43650
Polymers28,6622
Non-polymers1,77448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7240 Å2
ΔGint-312 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.870, 78.870, 36.788
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-9064-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / E.C.3.2.1.17 / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: C-TERMINAL CARBOXYLATE GROUP IS APPARENTLY PROTONATED
Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 256 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Na Acetate, pH 4.8, 7% NaCl, 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2005 / Details: mirrors
RadiationMonochromator: Double mirror monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 1.3→55.73 Å / Num. all: 29161 / Num. obs: 29161 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 27 % / Biso Wilson estimate: 10.43 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Χ2: 1.024 / Net I/σ(I): 10.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 15.9 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.92 / Num. unique all: 1416 / Rsym value: 0.52 / Χ2: 1.075 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: In-house model

Resolution: 1.3→55.73 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.18 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.04 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.145 1477 5.1 %RANDOM
Rwork0.103 ---
all0.105 29111 --
obs0.105 29111 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.981 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.023 Å
Refinement stepCycle: LAST / Resolution: 1.3→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 39 232 1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211111
X-RAY DIFFRACTIONr_bond_other_d0.0060.02815
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9181503
X-RAY DIFFRACTIONr_angle_other_deg1.1413.0081942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17922.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70715194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1171515
X-RAY DIFFRACTIONr_chiral_restr0.1220.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_nbd_refined0.2680.2273
X-RAY DIFFRACTIONr_nbd_other0.230.2956
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2544
X-RAY DIFFRACTIONr_nbtor_other0.0850.2607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3630.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.234
X-RAY DIFFRACTIONr_mcbond_it3.6033662
X-RAY DIFFRACTIONr_mcbond_other2.7233276
X-RAY DIFFRACTIONr_mcangle_it4.5251064
X-RAY DIFFRACTIONr_scbond_it6.9847474
X-RAY DIFFRACTIONr_scangle_it8.32510430
X-RAY DIFFRACTIONr_rigid_bond_restr3.47532065
X-RAY DIFFRACTIONr_sphericity_free17.0313251
X-RAY DIFFRACTIONr_sphericity_bonded7.05731898
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 97 -
Rwork0.116 2019 -
obs-2116 100 %

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