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- PDB-3qe8: Crystal Structure Analysis of Lysozyme-bound fac-[Re(CO)3(H2O)(Im)]+ -

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Basic information

Entry
Database: PDB / ID: 3qe8
TitleCrystal Structure Analysis of Lysozyme-bound fac-[Re(CO)3(H2O)(Im)]+
ComponentsLysozyme C
KeywordsHYDROLASE / RHENIUM COMPLEX / METALLATION
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
Tricarbonyl (aqua) (imidazole) rhenium(I) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsZobi, F. / Spingler, B.
CitationJournal: Inorg.Chem. / Year: 2012
Title: Post-protein-binding reactivity and modifications of the fac-[Re(CO)3]+ core
Authors: Zobi, F. / Spingler, B.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6059
Polymers28,6622
Non-polymers9437
Water3,045169
1
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8124
Polymers14,3311
Non-polymers4803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7945
Polymers14,3311
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.896, 77.996, 80.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-REI / Tricarbonyl (aqua) (imidazole) rhenium(I)


Mass: 356.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O4Re
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.01 Å3/Da / Density % sol: 38.81 % / Description: SF FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.54
Details: 0.05M acetate buffer pH 4.54, 0.9M NaCl, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2010
Details: MIRROR, BARTELS MONOCHROMATOR, DUAL CHANNEL CUT CRYSTALS, TOROIDAL MIRROR
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→55.874 Å / Num. obs: 57107 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 4.06 % / Rmerge(I) obs: 0.0055 / Rsym value: 0.0361 / Net I/σ(I): 16.76
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.28 / % possible all: 77.2

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IEE

1iee


Resolution: 1.49→55.87 Å / Num. parameters: 8857 / Num. restraintsaints: 8383 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE SF FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1372 2 %RANDOM
all0.197 68448 --
obs0.197 -93.8 %-
Displacement parametersBiso mean: 21.9583 Å2
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2199.8
Refinement stepCycle: LAST / Resolution: 1.49→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 37 169 2208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.084
X-RAY DIFFRACTIONs_approx_iso_adps0

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