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- PDB-7bmp: HEWL in cesium chloride (0.25 M CsCl in protein buffer and cryo p... -

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Basic information

Entry
Database: PDB / ID: 7bmp
TitleHEWL in cesium chloride (0.25 M CsCl in protein buffer 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
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 1.1Nov 13, 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)15,66918
Polymers14,3311
Non-polymers1,33817
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-282 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.952, 78.952, 36.870
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-376-

HOH

21A-381-

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.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 132.905 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50 mM sodium acetate pH 4.5, 1.71 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.9→39.48 Å / Num. obs: 9678 / % possible obs: 100 % / Redundancy: 22.1 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.012 / Rrim(I) all: 0.058 / Net I/σ(I): 43.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 19.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.940.174123226190.9940.0390.17917100
9.11-39.480.039236311910.0080.046899.5

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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: 1.9→39.48 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.395 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 469 4.9 %RANDOM
Rwork0.1551 ---
obs0.157 9175 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.05 Å2 / Biso mean: 18.865 Å2 / Biso min: 10.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å2-0 Å2
2--0.36 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.9→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 23 132 1156
Biso mean--31.38 27.92 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191056
X-RAY DIFFRACTIONr_bond_other_d0.0020.02950
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9091429
X-RAY DIFFRACTIONr_angle_other_deg1.12632191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95922.552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18615176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7181513
X-RAY DIFFRACTIONr_chiral_restr0.1280.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021203
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02246
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 36 -
Rwork0.126 663 -
all-699 -
obs--100 %

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