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- PDB-7be0: X-ray structure of Hen Egg White Lysozyme with dirhodium tetraace... -

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Basic information

Entry
Database: PDB / ID: 7be0
TitleX-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (2)
ComponentsLysozyme
KeywordsHYDROLASE / Metallodrug / Metal/protein adduct / bimetallic compounds
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
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-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / NITRATE ION / Rhodium / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLoreto, D. / Merlino, A. / Ferraro, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer Research22587 Italy
CitationJournal: Int J Mol Sci / Year: 2021
Title: Unusual Structural Features in the Adduct of Dirhodium Tetraacetate with Lysozyme.
Authors: Loreto, D. / Ferraro, G. / Merlino, A.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,71421
Polymers14,3311
Non-polymers1,38320
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint10 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.948, 77.948, 37.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-207-

NO3

21AAA-207-

NO3

31AAA-374-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 154 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-RH / Rhodium / Rhodium


Mass: 102.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rh / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 37.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.62→26.99 Å / Num. obs: 15018 / % possible obs: 98.7 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.021 / Net I/σ(I): 56.7
Reflection shellResolution: 1.62→1.65 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 623 / CC1/2: 0.942 / Rpim(I) all: 0.152 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193l

193l


Resolution: 1.62→26.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.706 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2028 736 4.914 %
Rwork0.1646 14241 -
all0.166 --
obs-14977 98.656 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.263 Å20 Å20 Å2
2---0.263 Å20 Å2
3---0.525 Å2
Refinement stepCycle: LAST / Resolution: 1.62→26.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 68 136 1205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131100
X-RAY DIFFRACTIONr_bond_other_d0.0020.018947
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1040.0111
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.6821481
X-RAY DIFFRACTIONr_angle_other_deg1.6451.5852182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50821.09464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54415169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9691511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0811305
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02252
X-RAY DIFFRACTIONr_nbd_refined0.2250.2257
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.2952
X-RAY DIFFRACTIONr_nbtor_refined0.170.2537
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1640.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2820.223
X-RAY DIFFRACTIONr_nbd_other0.2770.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2860.242
X-RAY DIFFRACTIONr_mcbond_it1.8411.953537
X-RAY DIFFRACTIONr_mcbond_other1.6651.931529
X-RAY DIFFRACTIONr_mcangle_it2.3812.902666
X-RAY DIFFRACTIONr_mcangle_other2.3822.906667
X-RAY DIFFRACTIONr_scbond_it3.2172.318562
X-RAY DIFFRACTIONr_scbond_other3.2152.32563
X-RAY DIFFRACTIONr_scangle_it4.5443.378821
X-RAY DIFFRACTIONr_scangle_other4.5423.379822
X-RAY DIFFRACTIONr_lrange_it5.82924.3661323
X-RAY DIFFRACTIONr_lrange_other5.82824.3711324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.661-1.7070.234470.191959X-RAY DIFFRACTION94.9953
1.707-1.7560.199490.169977X-RAY DIFFRACTION99.1304
1.756-1.810.285530.167953X-RAY DIFFRACTION100
1.81-1.870.192390.159960X-RAY DIFFRACTION100
1.87-1.9350.209570.164892X-RAY DIFFRACTION99.8947
1.935-2.0080.216490.172882X-RAY DIFFRACTION100
2.008-2.090.253430.153835X-RAY DIFFRACTION100
2.09-2.1830.166400.146818X-RAY DIFFRACTION100
2.183-2.2890.19490.136772X-RAY DIFFRACTION100
2.289-2.4130.171300.137747X-RAY DIFFRACTION99.8715
2.413-2.5590.194330.138714X-RAY DIFFRACTION100
2.559-2.7350.144360.138657X-RAY DIFFRACTION100
2.735-2.9540.192400.148617X-RAY DIFFRACTION99.848
2.954-3.2350.236350.153583X-RAY DIFFRACTION99.8384
3.235-3.6150.174240.148528X-RAY DIFFRACTION99.8192
3.615-4.1710.193210.163487X-RAY DIFFRACTION100
4.171-5.1010.194170.18408X-RAY DIFFRACTION100
5.101-7.1830.199170.258329X-RAY DIFFRACTION100

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