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- PDB-5nbj: DLS Tetragonal - ReHEWL -

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Basic information

Entry
Database: PDB / ID: 5nbj
TitleDLS Tetragonal - ReHEWL
ComponentsLysozyme C
KeywordsHYDROLASE / Rhenium tricarbonyl / Hen egg white lysozyme / radiopharmaceutical development
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
RHENIUM / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.266 Å
AuthorsBrink, A. / Helliwell, J.R.
Funding support South Africa, 2items
OrganizationGrant numberCountry
National Research FoundationUID 84266 & 99139 South Africa
SASOL University Collaboration Initiative South Africa
CitationJournal: IUCrJ / Year: 2017
Title: New leads for fragment-based design of rhenium/technetium radiopharmaceutical agents.
Authors: Brink, A. / Helliwell, J.R.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.3Sep 18, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rsym_value
Revision 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Jan 17, 2024Group: 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
Item: _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
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,53521
Polymers14,3311
Non-polymers2,20420
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-133 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.890, 79.890, 37.000
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-379-

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
Details: Multiple coordination possibilities of fac-[Re(CO)3(H2O)3]+ to the HEWL protein
Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-RE / RHENIUM / Rhenium


Mass: 186.207 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Re
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7 / Details: 10% NaCl, NaOAc 0.04 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.266→39.95 Å / Num. obs: 32463 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.9
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 20 % / Rmerge(I) obs: 2.066 / Mean I/σ(I) obs: 1.7 / Num. unique all: 283 / Num. unique obs: 1660 / CC1/2: 0.556 / Rpim(I) all: 0.688 / Rrim(I) all: 1.722 / Rsym value: 2.066 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W1Y

2w1y


Resolution: 1.266→39.945 Å / SU ML: 0.15 / SU R Cruickshank DPI: 0.046 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.45
RfactorNum. reflection% reflection
Rfree0.1966 1638 5.05 %
Rwork0.1722 --
obs0.1734 32462 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.266→39.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 20 80 1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081034
X-RAY DIFFRACTIONf_angle_d1.1451395
X-RAY DIFFRACTIONf_dihedral_angle_d12.3369
X-RAY DIFFRACTIONf_chiral_restr0.05145
X-RAY DIFFRACTIONf_plane_restr0.005184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.266-1.30330.27341370.25382502X-RAY DIFFRACTION100
1.3033-1.34540.28011450.21542518X-RAY DIFFRACTION100
1.3454-1.39340.24161290.19982524X-RAY DIFFRACTION100
1.3934-1.44920.2541330.17812533X-RAY DIFFRACTION100
1.4492-1.51520.20991300.16782540X-RAY DIFFRACTION100
1.5152-1.59510.19231310.15482543X-RAY DIFFRACTION100
1.5951-1.6950.17591360.14442558X-RAY DIFFRACTION100
1.695-1.82590.19531670.1442528X-RAY DIFFRACTION100
1.8259-2.00960.21071270.15752577X-RAY DIFFRACTION100
2.0096-2.30040.16511360.15872586X-RAY DIFFRACTION100
2.3004-2.89810.19861460.18752616X-RAY DIFFRACTION100
2.8981-39.96490.18961210.17622799X-RAY DIFFRACTION100

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