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- PDB-3cb7: The crystallographic structure of the digestive lysozyme 2 from M... -

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Basic information

Entry
Database: PDB / ID: 3cb7
TitleThe crystallographic structure of the digestive lysozyme 2 from Musca domestica at 1.9 Ang.
ComponentsLys-rich lysozyme 2
KeywordsHYDROLASE / Digestive lysozyme 2 / Musca domestica / Glycosidase
Function / homology
Function and homology information


lysozyme / lysozyme activity
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / 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
ACETIC ACID / ISOPROPYL ALCOHOL / Lys-rich lysozyme 2
Similarity search - Component
Biological speciesMusca domestica (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCancado, F.C. / Valerio, A.A. / Marana, S.R. / Barbosa, J.A.R.G.
Citation
Journal: To be Published
Title: The crystallographic structure of the digestive lysozyme 2 from Musca domestica at 1.9 Ang.
Authors: Marana, S.R. / Cancado, F.C. / Valerio, A.A. / Ferreira, C. / Terra, W.R. / Barbosa, J.A.R.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization, data collection and phasing of two digestive lysozymes from Musca domestica
Authors: Marana, S.R. / Cancado, F.C. / Valerio, A.A. / Ferreira, C. / Terra, W.R. / Barbosa, J.A.R.G.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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: Lys-rich lysozyme 2
B: Lys-rich lysozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0038
Polymers28,6102
Non-polymers3926
Water5,026279
1
A: Lys-rich lysozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4854
Polymers14,3051
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lys-rich lysozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5174
Polymers14,3051
Non-polymers2123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.903, 96.400, 33.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lys-rich lysozyme 2


Mass: 14305.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musca domestica (house fly) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q7YT17, lysozyme
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 40.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: The 3 uL drop was formed by 1.5 uL of protein solution at 9.8 mg/mL in 10 mM MES pH 5.5 plus 1.3 uL of 28% 2-propanol, 0.115 M sodium citrate pH 4.2 and 21% PEG 4000 plus 0.2 uL of 0.2 M ...Details: The 3 uL drop was formed by 1.5 uL of protein solution at 9.8 mg/mL in 10 mM MES pH 5.5 plus 1.3 uL of 28% 2-propanol, 0.115 M sodium citrate pH 4.2 and 21% PEG 4000 plus 0.2 uL of 0.2 M ammonium acetate, 0.1 M sodium citrate pH 5.6 and 30% MPD., VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2006 / Details: mirrors
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 17698 / Num. obs: 17698 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1423 / % possible all: 74.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2fbd

2fbd


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.923 / SU B: 15.216 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25789 910 5.1 %RANDOM
Rwork0.18355 ---
all0.18732 17674 --
obs0.18732 17674 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.144 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å20 Å2
2---3.92 Å20 Å2
3---5.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 26 279 2311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222089
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9392833
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25924.58396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42815337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.912158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21476
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21516
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6681.51283
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07122025
X-RAY DIFFRACTIONr_scbond_it1.9493950
X-RAY DIFFRACTIONr_scangle_it2.7454.5808
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 54 -
Rwork0.373 969 -
obs--72.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6912-0.4030.27814.1725-1.02380.69990.0161-0.06540.08710.13210.0150.15180.00810.0565-0.0312-0.199-0.0111-0.0253-0.088-0.0405-0.131617.477-0.33120.696
23.5106-1.0897-0.07864.0058-0.31520.55810.03670.2594-0.0088-0.2527-0.13150.01690.0922-0.00710.0948-0.16070.0052-0.0086-0.07150.0008-0.21826.13721.1827.946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1266 - 126
2X-RAY DIFFRACTION2BB6 - 1266 - 126

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