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- PDB-6ro3: 2Yr-X: Lysozyme with Re Cluster 2 year on shelf -

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Basic information

Entry
Database: PDB / ID: 6ro3
Title2Yr-X: Lysozyme with Re Cluster 2 year on shelf
ComponentsLysozyme C
KeywordsANTIMICROBIAL PROTEIN / Radio-pharmaceuticals / organometallic complex
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
ACETATE ION / BROMIDE ION / Re4(mu3-OH)4(CO)12 / RHENIUM / fac-tricarbonyl-triaqua rhenium(I) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsBrink, A. / Helliwell, J.R.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation in South Africa99139 South Africa
CitationJournal: Iucrj / Year: 2019
Title: Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging.
Authors: Brink, A. / Helliwell, J.R.
History
DepositionMay 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: 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)19,10216
Polymers14,3311
Non-polymers4,77015
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Data collection has been optimised to the rhenium anomalous dispersion signal to a large value (f " of 12.1 electrons) at its L1 absorption edge with a selected X-ray wavelength of 0.9763 ...Evidence: Data collection has been optimised to the rhenium anomalous dispersion signal to a large value (f " of 12.1 electrons) at its L1 absorption edge with a selected X-ray wavelength of 0.9763 angstrom. Rhenium complex coordination support by Infrared Spectroscopy.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-63 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.940, 79.940, 36.460
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-364-

HOH

21A-411-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 8 types, 135 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-RE / RHENIUM


Mass: 186.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Re
#5: Chemical ChemComp-KBW / Re4(mu3-OH)4(CO)12


Mass: 1144.947 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12O16Re4
#6: Chemical ChemComp-RRE / fac-tricarbonyl-triaqua rhenium(I)


Mass: 318.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3O6Re
#7: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: Standard hen egg white lysozyme (20 mg) crystallisation conditions were used of 10% NaCl, NaOAc 0.04 M (pH 4.7) and the fac-[Et4N]2[Re(CO)3(Br)3] at 0.03 M in 1.4 ml water, in sitting drop ...Details: Standard hen egg white lysozyme (20 mg) crystallisation conditions were used of 10% NaCl, NaOAc 0.04 M (pH 4.7) and the fac-[Et4N]2[Re(CO)3(Br)3] at 0.03 M in 1.4 ml water, in sitting drop conditions, initially included with DMSO (at 7.5 % v/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.03→39.97 Å / Num. obs: 55335 / % possible obs: 94.04 % / Redundancy: 11.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 38.7
Reflection shellResolution: 1.03→1.067 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.1646 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3732 / CC1/2: 0.897 / % possible all: 64.31

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W1Y

2w1y


Resolution: 1.03→39.97 Å / SU ML: 0.04 / SU R Cruickshank DPI: 0.018 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 7.91
RfactorNum. reflection% reflection
Rfree0.1178 2834 5.12 %
Rwork0.1111 --
obs0.1115 55334 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 10.64 Å2
Refinement stepCycle: LAST / Resolution: 1.03→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 127 120 1248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081227
X-RAY DIFFRACTIONf_angle_d1.7641784
X-RAY DIFFRACTIONf_dihedral_angle_d12.539451
X-RAY DIFFRACTIONf_chiral_restr0.093166
X-RAY DIFFRACTIONf_plane_restr0.007199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.04780.1351860.13291628X-RAY DIFFRACTION59
1.0478-1.06680.13651140.11631905X-RAY DIFFRACTION69
1.0668-1.08730.12271090.10982125X-RAY DIFFRACTION77
1.0873-1.10950.10441150.09632340X-RAY DIFFRACTION84
1.1095-1.13370.11031570.09492494X-RAY DIFFRACTION92
1.1337-1.160.09181410.08722682X-RAY DIFFRACTION97
1.16-1.1890.09361540.08482766X-RAY DIFFRACTION100
1.189-1.22120.09171420.08612755X-RAY DIFFRACTION100
1.2212-1.25710.10671450.08622782X-RAY DIFFRACTION100
1.2571-1.29770.0921570.08832733X-RAY DIFFRACTION100
1.2977-1.34410.09441470.08372784X-RAY DIFFRACTION100
1.3441-1.39790.09471520.0832781X-RAY DIFFRACTION100
1.3979-1.46150.10021650.08242765X-RAY DIFFRACTION100
1.4615-1.53860.09861300.08222800X-RAY DIFFRACTION100
1.5386-1.6350.09721510.08642781X-RAY DIFFRACTION100
1.635-1.76120.10461470.09482824X-RAY DIFFRACTION100
1.7612-1.93850.11891490.11152822X-RAY DIFFRACTION100
1.9385-2.2190.12661600.12072825X-RAY DIFFRACTION100
2.219-2.79560.1371540.1332875X-RAY DIFFRACTION100
2.7956-40.00010.14861590.15663033X-RAY DIFFRACTION100

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