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- PDB-7bmt: HEWL in sodium chloride -

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Basic information

Entry
Database: PDB / ID: 7bmt
TitleHEWL in sodium chloride
ComponentsLysozyme
KeywordsHYDROLASE / Cesium / Phasing
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
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 / SAD / Resolution: 1.47 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

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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)15,09920
Polymers14,3311
Non-polymers76819
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-120 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.877, 78.877, 36.960
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-399-

HOH

21A-473-

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 / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 38.67 %
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, 15 % (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.47→19.13 Å / Num. obs: 20426 / % possible obs: 99.6 % / Redundancy: 50.9 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.006 / Rrim(I) all: 0.043 / Net I/σ(I): 84.9
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
1.47-1.4926.40.147241759140.9930.0280.1521.693.1
8.04-19.1339.90.026605915210.0040.027138.493.8

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
SHELXDEphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.47→19.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.799 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 994 4.9 %RANDOM
Rwork0.1406 ---
obs0.142 19390 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.6 Å2 / Biso mean: 10.855 Å2 / Biso min: 4.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.47→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 35 178 1214
Biso mean--20.37 24.63 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021117
X-RAY DIFFRACTIONr_bond_other_d0.0040.021016
X-RAY DIFFRACTIONr_angle_refined_deg2.5181.9151517
X-RAY DIFFRACTIONr_angle_other_deg1.23932357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14422.80757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86715191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8651514
X-RAY DIFFRACTIONr_chiral_restr0.170.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021277
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02257
LS refinement shellResolution: 1.47→19.13 Å
RfactorNum. reflection% reflection
Rfree0.1687 994 4.9 %
Rwork0.1406 19390 -
obs--99.54 %

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