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- PDB-5a3z: Structure of monoclinic Lysozyme obtained by multi crystal data c... -

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Basic information

Entry
Database: PDB / ID: 5a3z
TitleStructure of monoclinic Lysozyme obtained by multi crystal data collection
ComponentsLYSOZYME
KeywordsHYDROLASE / MULTI CRYSTAL DATA COLLECTION / SYNCHROTRON SERIAL CRYSTALLOGRAPHY / SSX
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
NITRATE ION / Lysozyme C / Lysozyme C
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.59 Å
AuthorsZander, U. / Bourenkov, G. / Popov, A.N. / de Sanctis, D. / McCarthy, A.A. / Svensson, O. / Round, E.S. / Gordeliy, V.I. / Mueller-Dieckmann, C. / Leonard, G.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines.
Authors: Zander, U. / Bourenkov, G. / Popov, A.N. / De Sanctis, D. / Svensson, O. / Mccarthy, A.A. / Round, E. / Gordeliy, V. / Mueller-Dieckmann, C. / Leonard, G.A.
History
DepositionJun 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Source and taxonomy
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7315
Polymers32,5152
Non-polymers2163
Water3,261181
1
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3202
Polymers16,2581
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4123
Polymers16,2581
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.583, 62.638, 59.553
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 129 / Label seq-ID: 19 - 147

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.973359, -0.142323, -0.17977), (0.161863, 0.981824, 0.0991), (0.162398, -0.125558, 0.978704)15.73494, 3.27976, 35.83248

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Components

#1: Protein LYSOZYME / LYSOZYME C


Mass: 16257.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: B8YK79, UniProt: P00698*PLUS, lysozyme
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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

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Sample preparation

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→19.73 Å / Num. obs: 23004 / % possible obs: 85 % / Observed criterion σ(I): 2.2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08

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Processing

SoftwareName: REFMAC / Version: 5.8.0103 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.59→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.069 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26505 1182 5.1 %RANDOM
Rwork0.21311 ---
obs0.21565 21804 84.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.302 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20.59 Å2
2---0.81 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 14 181 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192075
X-RAY DIFFRACTIONr_bond_other_d0.0310.021894
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9072810
X-RAY DIFFRACTIONr_angle_other_deg1.24234313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6745258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53722.97101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63415333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0251522
X-RAY DIFFRACTIONr_chiral_restr0.080.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022442
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02548
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_it1.0241.5981035
X-RAY DIFFRACTIONr_mcbond_other1.0211.5951034
X-RAY DIFFRACTIONr_mcangle_it1.8212.3881292
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0931.751040
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.592→1.633 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 90 -
Rwork0.313 1470 -
obs--77.57 %

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