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- PDB-6a4p: HEWL crystals soaked in 2.5M GuHCl for 40 minutes -

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Basic information

Entry
Database: PDB / ID: 6a4p
TitleHEWL crystals soaked in 2.5M GuHCl for 40 minutes
ComponentsLysozyme C
KeywordsHYDROLASE / Protein Unfolding / Chemical denaturant / guanidine / Lysozyme
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
GUANIDINE / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsTushar, R. / Kini, R.M. / Koh, C.Y. / Hosur, M.V.
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
Title: X-ray crystallographic analysis of time-dependent binding of guanidine hydrochloride to HEWL: First steps during protein unfolding.
Authors: Raskar, T. / Koh, C.Y. / Niebling, S. / Kini, R.M. / Hosur, M.V.
History
DepositionJun 20, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 13, 2019ID: 5H6D
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,05115
Polymers14,3311
Non-polymers72014
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.280, 78.280, 36.960
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-332-

HOH

21A-441-

HOH

31A-452-

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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: The concentration of the protein was 20mg/ml. The precipitant solution in the reservoir was 0.1 M sodium acetate/acetic acid buffer of pH 4.6 to 5.0 containing 1.2 to 1.5M sodium chloride. ...Details: The concentration of the protein was 20mg/ml. The precipitant solution in the reservoir was 0.1 M sodium acetate/acetic acid buffer of pH 4.6 to 5.0 containing 1.2 to 1.5M sodium chloride. The soaking solution was 0.1M sodium acetate/acetic acid buffer at pH 3.5 containing 1.4M NaCl, 25% v/v glycerol (as cryo-protectant) and 2.5M of guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→55.35 Å / Num. obs: 10506 / % possible obs: 87.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 14.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.38
Reflection shellResolution: 1.76→1.818 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.76→55.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.705 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19823 527 5 %RANDOM
Rwork0.16637 ---
obs0.16886 9979 87.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0 Å2
2--0.2 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.76→55.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 44 165 1199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191048
X-RAY DIFFRACTIONr_bond_other_d0.0050.02980
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.921412
X-RAY DIFFRACTIONr_angle_other_deg0.77432184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9522.85749
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01215161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7431511
X-RAY DIFFRACTIONr_chiral_restr0.0640.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
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_it0.691.263515
X-RAY DIFFRACTIONr_mcbond_other0.691.265516
X-RAY DIFFRACTIONr_mcangle_it1.1681.892643
X-RAY DIFFRACTIONr_mcangle_other1.1681.895644
X-RAY DIFFRACTIONr_scbond_it0.8591.457533
X-RAY DIFFRACTIONr_scbond_other0.8581.459534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4852.105769
X-RAY DIFFRACTIONr_long_range_B_refined4.04511.7271375
X-RAY DIFFRACTIONr_long_range_B_other3.70411.0331307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.755→1.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 8 -
Rwork0.303 189 -
obs--22.8 %

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