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- PDB-7bms: HEWL in cesium chloride (1.5 M CsCl in crystallization condition ... -

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Basic information

Entry
Database: PDB / ID: 7bms
TitleHEWL in cesium chloride (1.5 M CsCl in crystallization condition and cryo protectant)
ComponentsLysozyme
KeywordsHYDROLASE / Cesium / Phasing
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKoelmel, W. / Kuper, J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KI 562/11-2 Germany
CitationJournal: Sci Rep / Year: 2021
Title: Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem.
Authors: Koelmel, W. / Kuper, J. / Kisker, C.
History
DepositionJan 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,66222
Polymers14,3311
Non-polymers2,33021
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-511 kcal/mol
Surface area6240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.928, 75.928, 35.707
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-341-

HOH

21A-394-

HOH

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Components

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 132.905 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.8 Å3/Da / Density % sol: 31.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 50 mM sodium acetate pH 4.5, 1.5 M cesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.71075 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71075 Å / Relative weight: 1
ReflectionResolution: 1.75→37.96 Å / Num. obs: 10988 / % possible obs: 99.6 % / Redundancy: 20.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.033 / Rrim(I) all: 0.161 / Net I/σ(I): 18.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.787.40.42141135560.9020.1660.4544.595.2
9.09-37.9620.30.17222361100.9950.0370.17726.699.5

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→37.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.341 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 583 5.3 %RANDOM
Rwork0.1748 ---
obs0.1766 10370 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.8 Å2 / Biso mean: 16.969 Å2 / Biso min: 9.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å2-0 Å2
2--0.56 Å2-0 Å2
3----1.11 Å2
Refinement stepCycle: final / Resolution: 1.75→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 24 131 1155
Biso mean--33.53 23.72 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0191064
X-RAY DIFFRACTIONr_bond_other_d0.0040.02951
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.9031445
X-RAY DIFFRACTIONr_angle_other_deg1.25532195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32722.40754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29515177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4891514
X-RAY DIFFRACTIONr_chiral_restr0.1560.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021222
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02252
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 44 -
Rwork0.192 708 -
all-752 -
obs--94.71 %

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