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- PDB-9gcv: Identification of chloride ions in lysozyme at long wavelengths -

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Basic information

Entry
Database: PDB / ID: 9gcv
TitleIdentification of chloride ions in lysozyme at long wavelengths
ComponentsLysozyme C
KeywordsHYDROLASE / 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: 2.703 Å
AuthorsEl Omari, K. / Forsyth, I. / Orr, C.M. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Utilizing anomalous signals for element identification in macromolecular crystallography.
Authors: El Omari, K. / Forsyth, I. / Duman, R. / Orr, C.M. / Mykhaylyk, V. / Mancini, E.J. / Wagner, A.
History
DepositionAug 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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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)14,5317
Polymers14,3311
Non-polymers2006
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-59 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.031, 79.031, 36.897
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-309-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: 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.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate pH 4.6, 1 M NaCl and 25% ethylene glycol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
1801N
2801N
3801N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2314.1328
SYNCHROTRONDiamond I2324.592
SYNCHROTRONDiamond I2335.166
Detector
TypeIDDetectorDate
DECTRIS PILATUS 12M1PIXELJul 31, 2024
DECTRIS PILATUS 12M2PIXELJul 31, 2024
DECTRIS PILATUS 12M3PIXELJul 31, 2024
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
14.13281
24.5921
35.1661
Reflection

Entry-ID: 9GCV / CC1/2: 0.99

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rrim(I) allDiffraction-IDNet I/σ(I)
2.7-79268076.817.70.07162
3-79.6198076.717.40.08244.4
3.37-79142177.417.10.09336.1
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.7-2.7518.91020.990.12160.4
3-3.0521.6640.990.0822
3.37-3.4336.1530.990.0723

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.703→55.884 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.845 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2171 138 5.188 %
Rwork0.1876 2522 -
all0.189 --
obs-2660 76.305 %
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: 19.357 Å2
Baniso -1Baniso -2Baniso -3
1-0.067 Å2-0 Å2-0 Å2
2--0.067 Å2-0 Å2
3----0.134 Å2
Refinement stepCycle: LAST / Resolution: 2.703→55.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 6 19 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121025
X-RAY DIFFRACTIONr_ext_dist_refined_b00.014117
X-RAY DIFFRACTIONr_angle_refined_deg1.761.7751389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.242511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56210166
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.2951050
X-RAY DIFFRACTIONr_chiral_restr0.120.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02819
X-RAY DIFFRACTIONr_nbd_refined0.2130.2462
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.230
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0740.29
X-RAY DIFFRACTIONr_mcbond_it1.2781.8515
X-RAY DIFFRACTIONr_mcangle_it2.1863.227642
X-RAY DIFFRACTIONr_scbond_it2.3452.032510
X-RAY DIFFRACTIONr_scangle_it3.8653.639747
X-RAY DIFFRACTIONr_lrange_it6.29122.4744517
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.703-2.7730.34860.2571350.2612500.9560.96356.40.228
2.773-2.8490.52790.261540.2722520.8780.96364.68250.233
2.849-2.9320.24370.2481460.2482230.9810.96768.60990.245
2.932-3.0210.3570.2431520.2472360.9410.96867.37290.235
3.021-3.120.2780.2121480.2152240.9830.97369.64290.196
3.12-3.2290.16270.1751370.1752050.9850.97970.24390.181
3.229-3.3510.22660.1891440.1912240.9910.97966.96430.186
3.351-3.4870.17580.2061340.2041990.9850.97471.35680.197
3.487-3.6420.418100.1781230.191890.9030.98470.37040.182
3.642-3.8190.18670.1771390.1781890.9890.98577.24870.175
3.819-4.0240.20770.1511370.1541820.9830.98779.12090.161
4.024-4.2670.16590.1511280.1521650.9870.98783.03030.153
4.267-4.5590.13460.1441370.1441630.9910.98787.73010.155
4.559-4.9220.28290.1851320.191560.9650.98290.38460.196
4.922-5.3880.19780.1491130.1531380.9830.98587.68120.152
5.388-6.0170.12880.2341240.2261320.9950.9731000.242
6.017-6.9340.1560.2061060.2031150.9820.97897.39130.222
6.934-8.460.19650.199960.1991010.990.9751000.213
8.46-11.8290.13830.139820.139860.9970.98598.83720.16
11.829-55.8840.09220.163550.165710.9821000.199

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