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- PDB-8dz7: Hen lysozyme in orthorhombic space group at ambient temperature -... -

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Basic information

Entry
Database: PDB / ID: 8dz7
TitleHen lysozyme in orthorhombic space group at ambient temperature - diffuse scattering dataset
ComponentsLysozyme C
KeywordsHYDROLASE / ROOM TEMPERATURE / DIFFUSE SCATTERING / LYSOZYME
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 / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsMeisburger, S.P. / Imran, S.M.S. / Ando, N.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117757 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124847 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
Citation
Journal: Nat Commun / Year: 2023
Title: Robust total X-ray scattering workflow to study correlated motion of proteins in crystals.
Authors: Meisburger, S.P. / Case, D.A. / Ando, N.
#1: Journal: Biorxiv / Year: 2022
Title: Robust total X-ray scattering workflow to study correlated motion of proteins in crystals
Authors: Meisburger, S.P. / Case, D.A. / Ando, N.
History
DepositionAug 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,3903
Polymers14,3311
Non-polymers582
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.486, 56.401, 73.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 318 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Reservoir contained 1.0-1.1 M NaCl, 0.1 M NaOAc pH 4.6. Drops of 30 microliters contained a 1:2 ratio of 90-100 mg/mL protein and reservoir solution.
Temp details: The trays were set up at room temperature, incubated at 45 degC until crystals appeared, then returned to room temperature

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2016 / Details: 100 micron collimator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.34→44.82 Å / Num. obs: 28707 / % possible obs: 96.9 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.011 / Rrim(I) all: 0.041 / Χ2: 1.02 / Net I/σ(I): 36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
7.32-44.8210.80.05965.82290.9980.0180.0621.6299.7
1.34-1.362.20.2383.89690.8980.170.2950.9268.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
XDS20200131data reduction
Coot0.9.5model building
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wtm

1wtm


Resolution: 1.34→44.82 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.029 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1362 1417 4.949 %
Rwork0.1179 27215 -
all0.119 --
obs-28632 96.756 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0 Å20 Å2
2--0.356 Å2-0 Å2
3----0.354 Å2
Refinement stepCycle: LAST / Resolution: 1.34→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 2 50 1053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0121053
X-RAY DIFFRACTIONr_bond_other_d0.0010.018965
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.6331432
X-RAY DIFFRACTIONr_angle_other_deg2.0251.5962200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96320.75866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27615172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2771512
X-RAY DIFFRACTIONr_chiral_restr0.1570.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021261
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02295
X-RAY DIFFRACTIONr_nbd_refined0.2660.2200
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.2874
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2534
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.218
X-RAY DIFFRACTIONr_metal_ion_refined0.4670.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2840.22
X-RAY DIFFRACTIONr_nbd_other0.2080.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0410.22
X-RAY DIFFRACTIONr_mcbond_it5.0082.016524
X-RAY DIFFRACTIONr_mcbond_other4.9712.007523
X-RAY DIFFRACTIONr_mcangle_it5.893.022656
X-RAY DIFFRACTIONr_mcangle_other5.9083.031657
X-RAY DIFFRACTIONr_scbond_it13.0362.705529
X-RAY DIFFRACTIONr_scbond_other13.0072.701529
X-RAY DIFFRACTIONr_scangle_it12.243.783774
X-RAY DIFFRACTIONr_scangle_other12.2013.779774
X-RAY DIFFRACTIONr_lrange_it8.02923.4811206
X-RAY DIFFRACTIONr_lrange_other8.03323.4331203
X-RAY DIFFRACTIONr_rigid_bond_restr22.39932018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.3720.237850.1991469X-RAY DIFFRACTION72.7528
1.372-1.4090.188990.1281786X-RAY DIFFRACTION89.4213
1.409-1.450.133940.0971852X-RAY DIFFRACTION94.466
1.45-1.4950.133990.0811830X-RAY DIFFRACTION98.7206
1.495-1.5440.106870.0741839X-RAY DIFFRACTION99.9481
1.544-1.5980.114900.0691793X-RAY DIFFRACTION99.8939
1.598-1.6580.111980.0671685X-RAY DIFFRACTION99.9439
1.658-1.7260.112930.0711641X-RAY DIFFRACTION100
1.726-1.8020.12710.0771610X-RAY DIFFRACTION100
1.802-1.890.162620.0841549X-RAY DIFFRACTION99.876
1.89-1.9920.122900.0921423X-RAY DIFFRACTION100
1.992-2.1130.15800.0991361X-RAY DIFFRACTION100
2.113-2.2590.142630.1061308X-RAY DIFFRACTION100
2.259-2.440.166570.1081219X-RAY DIFFRACTION100
2.44-2.6720.134480.1241134X-RAY DIFFRACTION100
2.672-2.9870.142600.141024X-RAY DIFFRACTION99.9078
2.987-3.4480.14460.147914X-RAY DIFFRACTION100
3.448-4.2210.123430.121776X-RAY DIFFRACTION100
4.221-5.960.115320.137627X-RAY DIFFRACTION100
5.96-44.820.169200.214374X-RAY DIFFRACTION99.4949

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