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- PDB-9ghx: Lysozyme covalently bound to fac-[Re(CO)3-imidazole] complex, inc... -

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Basic information

Entry
Database: PDB / ID: 9ghx
TitleLysozyme covalently bound to fac-[Re(CO)3-imidazole] complex, incubated for 112 weeks. Data collection done at mammalian body temperature.
ComponentsLysozyme C
KeywordsANTIMICROBIAL PROTEIN / C-type lysozyme / Lysozyme-like fold / Glycoside hydrolase / Rhenium tricarbonyl
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
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
IMIDAZOLE / RHENIUM / Tricarbonyl (aqua) (imidazole) rhenium(I) / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsJacobs, F.J.F. / Brink, A. / Helliwell, J.R.
Funding support South Africa, 3items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
Other governmentDHET Future Professors Program
Other privateSASOL University Collaboration Initiative
CitationJournal: Chem.Commun.(Camb.) / Year: 2024
Title: Body temperature protein X-ray crystallography at 37 °C: a rhenium protein complex seeking a physiological condition structure.
Authors: Jacobs, F.J.F. / Helliwell, J.R. / Brink, A.
History
DepositionAug 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)16,10312
Polymers14,3311
Non-polymers1,77111
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-54 kcal/mol
Surface area7260 Å2
Unit cell
Length a, b, c (Å)81.493, 81.493, 37.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-209-

RE

21A-321-

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 , 7 types, 38 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-VHL / Tricarbonyl di(imidazole) rhenium(I) / di(imidazol-1-yl)-tris(oxidaniumylidynemethyl)rhenium(1+)


Mass: 404.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N4O3Re
#4: Chemical ChemComp-REI / Tricarbonyl (aqua) (imidazole) rhenium(I)


Mass: 356.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O4Re
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-RE / RHENIUM


Mass: 186.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Re
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: HEWL, ReAA, Imidazole, 1.0 M NaCl, and 0.05 M sodium acetate at 4.5 pH.
Temp details: Room temperature (climate controled)

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Data collection

DiffractionMean temperature: 310.15 K
Ambient temp details: Data colletion conducted at mammalian body temperature
Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS DIAMOND MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 29, 2024
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.19→36.44 Å / Num. obs: 13693 / % possible obs: 99.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.1 Å2 / Rpim(I) all: 0.134 / Net I/σ(I): 5.64
Reflection shellResolution: 2.19→2.268 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 1276 / Rpim(I) all: 0.993 / % possible all: 95.49

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
APEXv2022.8-RC117data reduction
APEXv2022.8-RC117data collection
Aimless1.20.1-4487data scaling
PHASER1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→36.44 Å / SU ML: 0.3419 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2708 1205 9.87 %
Rwork0.2045 10999 -
obs0.2108 12204 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.81 Å2
Refinement stepCycle: LAST / Resolution: 2.19→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 59 27 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01541075
X-RAY DIFFRACTIONf_angle_d1.54891460
X-RAY DIFFRACTIONf_chiral_restr0.0626144
X-RAY DIFFRACTIONf_plane_restr0.0288187
X-RAY DIFFRACTIONf_dihedral_angle_d16.8172374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.280.40131190.31841108X-RAY DIFFRACTION90.22
2.28-2.380.33551390.29011218X-RAY DIFFRACTION97.7
2.38-2.510.30611350.27111246X-RAY DIFFRACTION99.42
2.51-2.660.31821340.25841236X-RAY DIFFRACTION100
2.66-2.870.29911320.23521249X-RAY DIFFRACTION99.78
2.87-3.160.24441350.20841238X-RAY DIFFRACTION100
3.16-3.610.24761390.18671230X-RAY DIFFRACTION99.71
3.62-4.550.251360.14751232X-RAY DIFFRACTION99.56
4.56-36.440.23731360.17461242X-RAY DIFFRACTION99.35

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