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- PDB-2fbd: The crystallographic structure of the digestive lysozyme 1 from M... -

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Basic information

Entry
Database: PDB / ID: 2fbd
TitleThe crystallographic structure of the digestive lysozyme 1 from Musca domestica at 1.90 Ang.
ComponentsLysozyme 1
KeywordsHYDROLASE / Digestive Lysozime / Musca domestica
Function / homology
Function and homology information


metabolic process / lysozyme / lysozyme activity
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
DI(HYDROXYETHYL)ETHER / Lysozyme 1
Similarity search - Component
Biological speciesMusca domestica (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCancado, F.C. / Marana, S.R. / Barbosa, J.A.R.G.
CitationJournal: 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. / Valero, A.A. / Ferreira, C. / Terra, W.R. / Barbosa, J.A.R.G.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1
B: Lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1577
Polymers27,6572
Non-polymers5005
Water5,603311
1
A: Lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1274
Polymers13,8281
Non-polymers2983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0313
Polymers13,8281
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Lysozyme 1
hetero molecules

B: Lysozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1577
Polymers27,6572
Non-polymers5005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area2250 Å2
ΔGint-42 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.523, 79.435, 45.203
Angle α, β, γ (deg.)90.00, 102.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysozyme 1 / / 1 / 4-beta-N-acetylmuramidase 1


Mass: 13828.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musca domestica (house fly) / Gene: AY344589 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q7YT16, lysozyme
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1% PEG 400, 0.1 M Na Hepes, 1.4 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 2003
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 19857 / Num. obs: 19857 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 5.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HEW

1hew


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.119 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19802 1016 5.1 %RANDOM
Rwork0.15333 ---
obs0.15565 18817 99.97 %-
all-18817 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.331 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å2-0.5 Å2
2---1.14 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 29 311 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212061
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9252799
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40523.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93915321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6911512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021576
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21232
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21481
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.51242
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14121980
X-RAY DIFFRACTIONr_scbond_it1.9873961
X-RAY DIFFRACTIONr_scangle_it2.7444.5819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 79 -
Rwork0.169 1348 -
obs--99.72 %
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)
11.06620.1662-0.38562.1979-0.96363.60070.0072-0.0516-0.05020.138-0.0183-0.0091-0.10540.02950.0111-0.1645-0.0079-0.0019-0.15440.0047-0.1177-1.32310.177318.3632
22.88490.91020.72531.60440.4961.6115-0.0066-0.0223-0.0301-0.07150.0258-0.0506-0.07870.0415-0.0191-0.134-0.01080.0166-0.15-0.0075-0.147312.2279-18.23691.6787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1221 - 122
2X-RAY DIFFRACTION2BB1 - 1221 - 122

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