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- PDB-6f1r: Tetragonal Lysozyme crystallized at 298 K and pH 4.5 with phospha... -

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Basic information

Entry
Database: PDB / ID: 6f1r
TitleTetragonal Lysozyme crystallized at 298 K and pH 4.5 with phosphate bound: control experiment
ComponentsLysozyme C
KeywordsHYDROLASE
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding.
Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A.
History
DepositionNov 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water2,918162
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-60 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.694, 78.694, 37.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

21A-330-

HOH

31A-458-

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.: 5 / 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.: 162 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.5 M Sodium Chloride, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationMonochromator: CHANNEL-CUT MONOCHROMATOR AND A KIRKPATRICK-BAEZ (KB) FOCUSING SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.1→18.83 Å / Num. obs: 48271 / % possible obs: 99.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 14.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.018 / Rrim(I) all: 0.05 / Net I/σ(I): 20.2 / Num. measured all: 396478 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.1-1.1280.60323780.9070.2230.644100
6.02-18.836.50.042670.9950.0170.04372.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E3U

4e3u


Resolution: 1.1→17.438 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 13.61
RfactorNum. reflection% reflection
Rfree0.1635 4553 4.99 %
Rwork0.1537 --
obs0.1542 48211 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.1 Å2 / Biso mean: 19.7966 Å2 / Biso min: 11.32 Å2
Refinement stepCycle: final / Resolution: 1.1→17.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 6 162 1156
Biso mean--23.62 27.78 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061025
X-RAY DIFFRACTIONf_angle_d0.9281393
X-RAY DIFFRACTIONf_chiral_restr0.077146
X-RAY DIFFRACTIONf_plane_restr0.006182
X-RAY DIFFRACTIONf_dihedral_angle_d14.841371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11250.16861670.198728583025100
1.1125-1.12560.17971550.191129083063100
1.1256-1.13930.19081910.176629103101100
1.1393-1.15370.22121530.17312811296499
1.1537-1.16890.17631850.17129023087100
1.1689-1.18490.19141800.154428633043100
1.1849-1.20180.17011650.152128923057100
1.2018-1.21980.19121570.150128963053100
1.2198-1.23880.17731410.147529293070100
1.2388-1.25910.14461450.138529293074100
1.2591-1.28080.16581350.139828843019100
1.2808-1.30410.14671430.135129533096100
1.3041-1.32920.15011290.137829103039100
1.3292-1.35630.17051570.138129103067100
1.3563-1.38580.18421530.136929023055100
1.3858-1.4180.151390.12829073046100
1.418-1.45350.13761300.130429673097100
1.4535-1.49270.12671640.121828493013100
1.4927-1.53660.12931730.124728773050100
1.5366-1.58620.1511480.125929333081100
1.5862-1.64290.12661470.125429083055100
1.6429-1.70860.12991200.129429363056100
1.7086-1.78630.17641620.139328873049100
1.7863-1.88030.19341580.146928783036100
1.8803-1.9980.19361380.148729193057100
1.998-2.1520.13311400.14482895303599
2.152-2.36810.15831440.14882918306299
2.3681-2.70970.15681620.164228603022100
2.7097-3.40970.15851510.1722874302599
3.4097-17.43970.19451210.17662550267187

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