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- PDB-6d6h: Triclinic lysozyme cryocooled to 100 K with 47% MPD as cryoprotectant -

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Basic information

Entry
Database: PDB / ID: 6d6h
TitleTriclinic lysozyme cryocooled to 100 K with 47% MPD as cryoprotectant
ComponentsLysozyme C
KeywordsHYDROLASE / Glycosidase
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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.00006383515 Å
AuthorsJuers, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R15GM090248 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.
Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z.
History
DepositionApr 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,00210
Polymers14,3311
Non-polymers6709
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.993, 31.687, 33.989
Angle α, β, γ (deg.)88.270, 71.251, 68.505
Int Tables number1
Space group name H-MP1
Space group name HallP1

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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


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
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: 1.78 Å3/Da / Density % sol: 30.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Protein: 10 mg/mL in water Well: 0.3 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→13.5 Å / Num. obs: 6475 / % possible obs: 97.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 6.69282807111 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.11 Å / Mean I/σ(I) obs: 9 / CC1/2: 0.671 / Rrim(I) all: 0.878

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALAdata scaling
CrysalisProdata collection
PHENIXphasing
RefinementResolution: 2.00006383515→13.1905599404 Å / SU ML: 0.175778276467 / Cross valid method: FREE R-VALUE / σ(F): 2.01104711027 / Phase error: 17.13903934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.192704653407 304 4.69860896445 %
Rwork0.125969681724 6166 -
obs0.128806872456 6470 97.3371445765 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.1145747538 Å2
Refinement stepCycle: LAST / Resolution: 2.00006383515→13.1905599404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 44 121 1166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002075292929981097
X-RAY DIFFRACTIONf_angle_d0.5283235893861484
X-RAY DIFFRACTIONf_chiral_restr0.0347665931927152
X-RAY DIFFRACTIONf_plane_restr0.00194144302733196
X-RAY DIFFRACTIONf_dihedral_angle_d11.134256084401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.5170.2081631631720.1270051557733092X-RAY DIFFRACTION98.6102719033
2.517-13.19080.1794950364651320.1252922152943074X-RAY DIFFRACTION96.0743182499

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