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- PDB-4w96: Crystal structure of cross-linked tetragonal hen egg white lysozy... -

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Basic information

Entry
Database: PDB / ID: 4w96
TitleCrystal structure of cross-linked tetragonal hen egg white lysozyme soaked with 5mM [Ru(CO)3Cl2]2 followed by the reaction in deoxy-myoglobin solution
ComponentsLysozyme C
KeywordsHYDROLASE
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
DIMETHYLFORMAMIDE / RUTHENIUM ION / bis(oxidaniumylidynemethyl)ruthenium(2+) / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsTabe, H. / Fujita, K. / Abe, S. / Tsujimoto, M. / Kuchimaru, T. / Kizaka-Kondo, S. / Takano, M. / Kitagawa, S. / Ueno, T.
CitationJournal: Inorg.Chem. / Year: 2015
Title: Preparation of a Cross-Linked Porous Protein Crystal Containing Ru Carbonyl Complexes as a CO-Releasing Extracellular Scaffold
Authors: Tabe, H. / Fujita, K. / Abe, S. / Tsujimoto, M. / Kuchimaru, T. / Kizaka-Kondoh, S. / Takano, M. / Kitagawa, S. / Ueno, T.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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)15,67720
Polymers14,3311
Non-polymers1,34519
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.011, 79.011, 36.994
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
11A-219-

RU

21A-306-

HOH

31A-313-

HOH

41A-362-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 6 types, 116 molecules

#2: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE / Dimethylformamide


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / 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: Chemical ChemComp-RU1 / bis(oxidaniumylidynemethyl)ruthenium(2+)


Mass: 157.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O2Ru
#6: Chemical
ChemComp-RU / RUTHENIUM ION / Ruthenium


Mass: 101.070 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ru
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 38.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: NaCl, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. obs: 17128 / % possible obs: 93.5 % / Redundancy: 11.9 % / Net I/σ(I): 58.8
Reflection shellResolution: 1.5→1.54 Å / % possible all: 99.14

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata reduction
MOLREPdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.513 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 928 5.1 %RANDOM
Rwork0.1945 17128 --
obs0.1961 17128 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.63 Å2 / Biso mean: 24.192 Å2 / Biso min: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 27 97 1125
Biso mean--34.7 30.24 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211039
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.9071406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10523.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07315167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4861511
X-RAY DIFFRACTIONr_chiral_restr0.1510.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02806
X-RAY DIFFRACTIONr_mcbond_it1.4521.5642
X-RAY DIFFRACTIONr_mcangle_it2.40221017
X-RAY DIFFRACTIONr_scbond_it3.4573397
X-RAY DIFFRACTIONr_scangle_it5.4764.5388
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 64 -
Rwork0.206 1315 -
all-1379 -
obs--99.14 %

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