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- PDB-5laf: Room temperature X-ray diffraction of tetragonal HEWL with 1M of ... -

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Basic information

Entry
Database: PDB / ID: 5laf
TitleRoom temperature X-ray diffraction of tetragonal HEWL with 1M of uridine. First data set (0.31 MGy)
ComponentsLysozyme C
KeywordsHYDROLASE / room temperature
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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsCastellvi, A. / Juanhuix, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Nuclear Safety Council Spain
CitationJournal: J Synchrotron Radiat / Year: 2017
Title: Uridine as a new scavenger for synchrotron-based structural biology techniques.
Authors: Crosas, E. / Castellvi, A. / Crespo, I. / Fulla, D. / Gil-Ortiz, F. / Fuertes, G. / Kamma-Lorger, C.S. / Malfois, M. / Aranda, M.A. / Juanhuix, J.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 2.0Jan 10, 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 2.1Nov 13, 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)14,4975
Polymers14,3311
Non-polymers1654
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-30 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.110, 79.110, 37.897
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-328-

HOH

21A-334-

HOH

31A-391-

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.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: protein: 50 mg/ml of HEWL in mQ crystallization solution: 200mM NaAcetate pH 4.7 + 10% NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9840019 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9840019 Å / Relative weight: 1
ReflectionResolution: 1.5→39.56 Å / Num. obs: 19787 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.791 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 5.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1BWH

1bwh


Resolution: 1.5→39.56 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.032 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17636 937 4.7 %RANDOM
Rwork0.1442 ---
obs0.14572 18810 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.736 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.5→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 91 1099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191055
X-RAY DIFFRACTIONr_bond_other_d0.0020.02969
X-RAY DIFFRACTIONr_angle_refined_deg2.3291.9071433
X-RAY DIFFRACTIONr_angle_other_deg1.19332210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22323.13751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1315172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2811511
X-RAY DIFFRACTIONr_chiral_restr0.1490.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02277
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1491.633531
X-RAY DIFFRACTIONr_mcbond_other1.921.623529
X-RAY DIFFRACTIONr_mcangle_it2.9632.448666
X-RAY DIFFRACTIONr_mcangle_other2.9862.453667
X-RAY DIFFRACTIONr_scbond_it4.1952.18524
X-RAY DIFFRACTIONr_scbond_other4.1922.182525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5563.071768
X-RAY DIFFRACTIONr_long_range_B_refined7.97415.051314
X-RAY DIFFRACTIONr_long_range_B_other7.97915.061315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 66 -
Rwork0.186 1367 -
obs--99.86 %

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