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- PDB-1am7: Lysozyme from bacteriophage lambda -

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Basic information

Entry
Database: PDB / ID: 1am7
TitleLysozyme from bacteriophage lambda
ComponentsLYSOZYME
KeywordsGLYCOSIDASE / TRANSGLYCOSYLASE / EVOLUTION / LYSOZYME
Function / homology
Function and homology information


: / lytic transglycosylase activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin lambda type / Phage lysozyme / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsEvrard, C. / Fastrez, J. / Declercq, J.P.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the lysozyme from bacteriophage lambda and its relationship with V and C-type lysozymes.
Authors: Evrard, C. / Fastrez, J. / Declercq, J.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of Bacteriophage Lambda Lysozyme in which All Tryptophans Have Been Replaced by Aza-Tryptophans
Authors: Evrard, C. / Declercq, J.-P. / Fastrez, J.
#2: Journal: Lysozymes: Model Enzymes in Biochemistry and Biology
Year: 1996
Title: Phage Lysozymes
Authors: Fastrez, J.
#3: Journal: Protein Eng. / Year: 1995
Title: Biosynthetic Incorporation of 7-Azatryptophan Into the Phage Lambda Lysozyme: Estimation of Tryptophan Accessibility, Effect on Enzymatic Activity and Protein Stability
Authors: Soumillion, P. / Jespers, L. / Vervoort, J. / Fastrez, J.
#4: Journal: Biochem.J. / Year: 1992
Title: A Large Decrease in Heat-Shock-Induced Proteolysis After Tryptophan Starvation Leads to Increased Expression of Phage Lambda Lysozyme Cloned in Escherichia Coli
Authors: Soumillion, P. / Fastrez, J.
#5: Journal: J.Mol.Biol. / Year: 1992
Title: Is the Bacteriophage Lambda Lysozyme an Evolutionary Link or a Hybrid between the C and V-Type Lysozymes? Homology Analysis and Detection of the Catalytic Amino Acid Residues
Authors: Jespers, L. / Sonveaux, E. / Fastrez, J.
#6: Journal: Protein Eng. / Year: 1991
Title: Overexpression of the Phage Lambda Lysozyme Cloned in Escherichia Coli: Use of a Degenerative Mixture of Synthetic Ribosome Binding Sites and Increase of the Protein Stability in Vivo
Authors: Jespers, L. / Sonveaux, E. / Fastrez, J. / Phanapoulos, A. / Davison, J.
History
DepositionJun 24, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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
B: LYSOZYME
C: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7496
Polymers53,5683
Non-polymers1803
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9162
Polymers17,8561
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9162
Polymers17,8561
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9162
Polymers17,8561
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.010, 78.800, 82.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.656304, -0.154706, -0.738465), (-0.080198, -0.958903, 0.272163), (-0.750222, 0.237845, 0.616925)122.5875, 93.2218, 29.2524
2given(0.92675, -0.138949, 0.349039), (-0.114118, -0.989306, -0.090832), (0.357928, 0.044347, -0.932696)6.5827, 130.2514, 9.8868

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Components

#1: Protein LYSOZYME


Mass: 17856.146 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Cellular location: CYTOPLASM / Gene: R / Plasmid: PLJ05 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): M5219 / References: UniProt: P03706, lysozyme
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 5.3
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M SODIUM CITRATE PH 5.3, 15% V/V 2-PROPANOL AND 20% W/ V PEG 4000.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: protein solution is mixed 50:50 with a well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mM1dropNaH2PO4
30.02 %(w/v)1dropNaN3
420 %(w/v)PEG40001reservoir
515 %(v/v)2-propanol1reservoir
60.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 3, 1995 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 21455 / % possible obs: 98.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 28.1 Å2 / Rsym value: 0.09 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.297 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 104257 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 93.5 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.0066 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1040 5 %RANDOM AND UNIFORM DISTRIBUTION
Rwork0.1627 ---
obs0.1627 20814 95.8 %-
Displacement parametersBiso mean: 25.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 0 130 3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.41.5
X-RAY DIFFRACTIONx_mcangle_it3.42
X-RAY DIFFRACTIONx_scbond_it2.92
X-RAY DIFFRACTIONx_scangle_it42.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 2.8 Å2 / Rms dev position: 0.058 Å / Weight Biso : 2
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.269 103 5 %
Rwork0.23 1863 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2ISO.PARISO.TOP
X-RAY DIFFRACTION3TRN.PARTRN.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9999 Å / σ(I): 1 / Rfactor obs: 0.1635
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27
LS refinement shell
*PLUS
Rfactor obs: 0.23

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