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- PDB-6rta: Tetragonal lysozyme grown with 300g/L Ficoll -

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Basic information

Entry
Database: PDB / ID: 6rta
TitleTetragonal lysozyme grown with 300g/L Ficoll
ComponentsLysozyme C
KeywordsHYDROLASE / Glycoside hydrolase
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPereira, P.J.B. / Ferreira, C. / Martins, P.M.
CitationJournal: Phys Chem Chem Phys / Year: 2020
Title: Protein crystals as a key for deciphering macromolecular crowding effects on biological reactions.
Authors: Ferreira, C. / Pinto, M.F. / Macedo-Ribeiro, S. / Pereira, P.J.B. / Rocha, F.A. / Martins, P.M.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 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.title / _citation.year
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4254
Polymers14,3311
Non-polymers943
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-29 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.662, 78.662, 37.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

21A-362-

HOH

31A-478-

HOH

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.2M Sodium Acetate pH 4.7, 3% (w/v) NaCl, 300 g/L Ficoll

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION GEMINI / Wavelength: 1.54056 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.8→14.61 Å / Num. obs: 11092 / % possible obs: 98.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.042 / Rrim(I) all: 0.093 / Net I/σ(I): 15.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 616 / Rpim(I) all: 0.51 / Rrim(I) all: 0.89 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W1X

2w1x


Resolution: 1.8→14.607 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 521 4.71 %
Rwork0.1644 --
obs0.1657 11064 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→14.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 182 1186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061067
X-RAY DIFFRACTIONf_angle_d0.7921450
X-RAY DIFFRACTIONf_dihedral_angle_d14.203644
X-RAY DIFFRACTIONf_chiral_restr0.051150
X-RAY DIFFRACTIONf_plane_restr0.004193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.9810.281120.23862519X-RAY DIFFRACTION96
1.981-2.26680.18351200.18422594X-RAY DIFFRACTION98
2.2668-2.85240.23611330.16552674X-RAY DIFFRACTION100
2.8524-14.60760.15681560.13832756X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.49490.60910.83141.14930.56143.27740.0307-0.12950.13480.1212-0.00380.0613-0.2361-0.1170.01490.13250.01260.04260.121-0.01770.161931.932223.130217.9364
24.79730.95920.96178.836-0.69580.6712-0.2396-0.36040.00590.00890.22740.4901-0.1199-0.23750.02720.07730.006-0.01720.2073-0.00950.176327.575215.72267.3521
31.89751.29610.06082.63810.27060.74650.0407-0.10710.012-0.0075-0.0207-0.0820.03520.02570.00710.10890.01120.02180.08940.00080.103839.681817.418514.9434
44.37470.23630.35371.21712.57386.33430.1336-0.04090.1265-0.22610.1241-0.66150.64710.1125-0.14620.24280.02990.06660.1241-0.02480.17554.002719.6694.3027
53.56180.93541.03361.5981-0.51050.8871-0.20860.3353-0.0497-0.2570.1514-0.02860.1764-0.16510.08730.159-0.03640.01320.1164-0.01370.098346.417322.68932.0666
65.06391.9528-0.61081.8938-0.39840.1037-0.22480.6142-0.0699-0.32440.17410.27380.20640.0782-0.03260.2144-0.05990.00390.3136-0.01840.108444.486125.2981-5.0176
72.16231.68160.63723.61140.57050.9163-0.1067-0.06010.2738-0.05480.0420.3506-0.0982-0.150.09670.11810.012-0.02080.12060.01470.144237.084225.35235.4439
83.4290.34642.70272.04230.30165.39640.00170.3101-0.1049-0.18760.0917-0.22520.03630.7355-0.07060.0999-0.00550.02630.1418-0.0010.121440.13229.58145.5943
94.3442-3.8958-4.18535.69374.81044.6232-0.00040.1208-0.0180.2059-0.05420.33330.0452-0.50460.1610.12710.03150.02530.17850.02430.135730.81310.66619.4717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 100 )
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 114 )
9X-RAY DIFFRACTION9chain 'A' and (resid 115 through 129 )

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