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- PDB-5kxp: Hen Egg White Lysozyme at 278K, Data set 2 -

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Basic information

Entry
Database: PDB / ID: 5kxp
TitleHen Egg White Lysozyme at 278K, Data set 2
ComponentsLysozyme C
KeywordsISOMERASE / Conformational variation / Radiation damage
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsRussi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110580 United States
National Science Foundation (NSF, United States)STC-1231306 United States
CitationJournal: J Synchrotron Radiat / Year: 2017
Title: Conformational variation of proteins at room temperature is not dominated by radiation damage.
Authors: Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,3542
Polymers14,3311
Non-polymers231
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.145, 79.145, 37.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (1.0 M SODIUM CHLORIDE, 50 MM SODIUM ACETATE PH 4.5) AND PROTEIN (40-60 MG/ML)

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.21549 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21549 Å / Relative weight: 1
ReflectionResolution: 1.198→31.41 Å / Num. all: 35868 / Num. obs: 35868 / % possible obs: 93.9 % / Redundancy: 3.5 % / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Rsym value: 0.109 / Net I/av σ(I): 1.945 / Net I/σ(I): 10 / Num. measured all: 125334
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.263.10.5191.31458747750.3120.6120.5192.286.8
1.26-1.343.40.35421731950270.2050.4120.3543.696.5
1.34-1.433.50.2462.61641446680.1420.2860.2465.395.3
1.43-1.553.60.1873.11559942930.1070.2170.1878.293.9
1.55-1.693.60.1463.61448239810.0840.170.14611.394.2
1.69-1.893.60.12441317236890.0710.1440.12414.296
1.89-2.193.60.1094.31185632620.0610.1260.10917.295.6
2.19-2.683.60.14.8999327600.0550.1150.118.795.5
2.68-3.793.60.0974.1783021730.0570.1130.09719.594.7
3.79-31.413.30.14.4408212400.0590.1180.118.193.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2BLX

2blx


Resolution: 1.2→31.41 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.945 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 1798 5 %RANDOM
Rwork0.1617 ---
obs0.1634 34044 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.51 Å2 / Biso mean: 14.225 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.2→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 1 84 1086
Biso mean--19.49 26.72 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021974
X-RAY DIFFRACTIONr_bond_other_d0.0020.021782
X-RAY DIFFRACTIONr_angle_refined_deg2.5051.9082765
X-RAY DIFFRACTIONr_angle_other_deg1.3293.0064118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04224.08693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75515318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9951514
X-RAY DIFFRACTIONr_chiral_restr0.1480.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022464
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02512
X-RAY DIFFRACTIONr_mcbond_it1.4011.255967
X-RAY DIFFRACTIONr_mcbond_other1.3581.252966
X-RAY DIFFRACTIONr_mcangle_it2.1651.8961273
LS refinement shellResolution: 1.198→1.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 121 -
Rwork0.258 2058 -
all-2179 -
obs--77.43 %

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