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- PDB-6o2h: Hen lysozyme in triclinic space group at ambient temperature - di... -

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Basic information

Entry
Database: PDB / ID: 6o2h
TitleHen lysozyme in triclinic space group at ambient temperature - diffuse scattering dataset
ComponentsLysozyme C
KeywordsHYDROLASE / Room Temperature / Diffuse Scattering / Lysozyme
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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.212 Å
AuthorsMeisburger, S.P. / 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 Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: Nat Commun / Year: 2020
Title: Diffuse X-ray scattering from correlated motions in a protein crystal.
Authors: Meisburger, S.P. / Case, D.A. / Ando, N.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 11, 2023Group: Refinement description / Category: 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)14,8019
Polymers14,3311
Non-polymers4698
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.424, 32.134, 34.513
Angle α, β, γ (deg.)88.657, 108.460, 111.877
Int Tables number1
Space group name H-MP1

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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-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.86 Å3/Da / Density % sol: 33.77 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.5
Details: 8 microliter drops with 5-15 mg/mL protein, 224-300 mM NaNO3, 50 mM NaOAc pH 4.5, under paraffin oil
Temp details: The trays were set up at room temperature, moved to 4 degC for 8-12 hours, and returned to room temperature.

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: Ambient / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2017 / Details: 100 micron collimator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 1.21→32.55 Å / Num. obs: 30111 / % possible obs: 96.1 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rpim(I) all: 0.025 / Net I/σ(I): 27.4
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 12.5 / Num. unique obs: 832 / CC1/2: 0.994 / Rpim(I) all: 0.038 / % possible all: 52.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSJun 1, 2017data reduction
Aimless0.5.29data scaling
Coot0.8.0-3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lzt

4lzt


Resolution: 1.212→32.548 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1172 1495 -
Rwork0.0968 --
all0.098 --
obs-30108 96.103 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.073 Å20.049 Å2-0.104 Å2
2--0.307 Å2-0.065 Å2
3----0.315 Å2
Refinement stepCycle: LAST / Resolution: 1.212→32.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 29 92 1122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0131184
X-RAY DIFFRACTIONr_bond_other_d0.0350.0181041
X-RAY DIFFRACTIONr_angle_refined_deg2.6041.6581619
X-RAY DIFFRACTIONr_angle_other_deg2.5761.5992422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39320.41173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28215200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1081514
X-RAY DIFFRACTIONr_chiral_restr0.1830.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021417
X-RAY DIFFRACTIONr_gen_planes_other0.0280.02290
X-RAY DIFFRACTIONr_nbd_refined0.2270.2191
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.2808
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2541
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.229
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.211
X-RAY DIFFRACTIONr_nbd_other0.1880.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2730.211
X-RAY DIFFRACTIONr_mcbond_it1.7620.932569
X-RAY DIFFRACTIONr_mcbond_other1.7310.924568
X-RAY DIFFRACTIONr_mcangle_it2.3841.411722
X-RAY DIFFRACTIONr_mcangle_other2.3991.417723
X-RAY DIFFRACTIONr_scbond_it4.0331.448615
X-RAY DIFFRACTIONr_scbond_other3.5971.39594
X-RAY DIFFRACTIONr_scangle_it4.2372.016886
X-RAY DIFFRACTIONr_scangle_other4.0151.944865
X-RAY DIFFRACTIONr_lrange_it3.89211.6991306
X-RAY DIFFRACTIONr_lrange_other3.83311.5481299
X-RAY DIFFRACTIONr_sphericity_free24.725575
X-RAY DIFFRACTIONr_sphericity_bonded9.77352209
X-RAY DIFFRACTIONr_rigid_bond_restr14.87332225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.212-1.2430.136750.0881332234460.02560.099
1.243-1.2770.102950.0751923223590.29080.084
1.277-1.3140.1041200.0682012219397.21840.078
1.314-1.3550.0911070.0582017212799.8590.068
1.355-1.3990.091040.05197920831000.061
1.399-1.4480.095910.05192620171000.062
1.448-1.5030.086980.051804190399.94740.064
1.503-1.5640.0841070.054173418411000.068
1.564-1.6330.077930.054169217851000.067
1.633-1.7130.079810.055163617171000.07
1.713-1.8050.08750.061520159699.93730.076
1.805-1.9140.107720.075147715491000.098
1.914-2.0460.098600.081136514251000.106
2.046-2.2090.097610.085126813291000.114
2.209-2.4190.131620.093117712391000.127
2.419-2.7030.144560.108106411201000.142
2.703-3.1170.104410.1199449851000.158
3.117-3.8090.153460.1387928381000.175
3.809-5.350.192290.1996096381000.201
5.35-32.5480.228220.27734236599.7260.299

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