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- PDB-1lcn: Monoclinic hen egg white lysozyme, thiocyanate complex -

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Basic information

Entry
Database: PDB / ID: 1lcn
TitleMonoclinic hen egg white lysozyme, thiocyanate complex
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / GLYCOSIDASE / LYSOZYME
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
THIOCYANATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsHamiaux, C. / Prange, T. / Ducruix, A. / Vaney, M.C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structural effects of monovalent anions on polymorphic lysozyme crystals.
Authors: Vaney, M.C. / Broutin, I. / Retailleau, P. / Douangamath, A. / Lafont, S. / Hamiaux, C. / Prange, T. / Ducruix, A. / Ries-Kautt, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The Decameric Structure of Bovine Pancreatic Trypsin Inhibitor (BPTI) at 2.7 A Resolution.
Authors: Hamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structures of Monoclinic Lysozyme Iodide at 1.6 A and of Triclinic Lysozyme Nitrate at 1.1 A
Authors: Steinhauf, L.K.
#3: Journal: Biophys.Chem. / Year: 1998
Title: Characterization of the Interaction Between Bovine Pancreatic Trypsin Inhibitor and Thiocyanate by NMR
Authors: Jolivalt, C. / Bockmann, A. / Ries-Kautt, M. / Ducruix, A. / Guittet, E.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of Hexagonal Turkey Egg-White Lysozyme at 1.65 A Resolution
Authors: Howell, P.L.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of a Dimeric Form of Erabutoxin-B, Crystallized from a Thiocyanate Solution
Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A.
#6: Journal: J.Cryst.Growth / Year: 1991
Title: Crystallisation of Basic Proteins by Ion Pairing
Authors: Ries-Kautt, M. / Ducruix, A.
History
DepositionOct 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (LYSOZYME)
B: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8375
Polymers28,6622
Non-polymers1743
Water2,450136
1
A: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4473
Polymers14,3311
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3892
Polymers14,3311
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.010, 63.180, 60.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97654, 0.1823, -0.11462), (-0.19144, 0.97868, -0.07443), (0.09861, 0.09463, 0.99062)
Vector: -16.78495, 2.84472, 26.00986)

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Components

#1: Protein PROTEIN (LYSOZYME) / MURAMIDASE


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: SIGMA, USED AFTER ION-EXCHANGE PURIFICATION (DESALTING)
Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsLOOP 67-73 STANDS IN TWO DIFFERENT CONFORMATIONS IN MOLECULES A AND B, AND IS BETTER DEFINED IN ...LOOP 67-73 STANDS IN TWO DIFFERENT CONFORMATIONS IN MOLECULES A AND B, AND IS BETTER DEFINED IN MOLECULE A. ARG B 73 PLAYS AN IMPORTANT ROLE IN THE ALTERNATE CONFORMATION IN MOLECULE B: BEING INVOLVED IN A SALT BRIDGE WITH ASP B119 (OF A SYMMETRY RELATED MOLECULE), IT STANDS IN A DISALLOWED REGION OF THE RAMACHANDRAN PLOT. ALLOWS THE LOOP TO ADOPT ANOTHER CONFORMATION.
Has protein modificationY
Nonpolymer details3 THIOCYANATE ANIONS ARE FOUND IN THE STRUCTURE. THEY ARE SPREAD OVER TWO SITES: SCN201 IS BOUND TO ...3 THIOCYANATE ANIONS ARE FOUND IN THE STRUCTURE. THEY ARE SPREAD OVER TWO SITES: SCN201 IS BOUND TO TYR B53, BUT NO DENSITY IS FOUND AT ITS EQUIVALENT POSITION IN MOLECULE A. SCN202 AND 203 ARE FOUND AT EQUIVALENT POSITION IN MOLECULE A AND B, BOUND TO LYS 116.

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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: 1.9 Å3/Da / Density % sol: 33 %
Crystal growpH: 5 / Details: KSCN 190MM BUFFER CH3COOK 50MM, PH=5, pH 5.0
Crystal grow
*PLUS
Temperature: 291 K / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.7 mg/mlprotein1drop
250 mMpotassium acetate1drop
3190 mM1dropKSCN

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.963
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 1998 / Details: MIRROR
RadiationMonochromator: BENT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.963 Å / Relative weight: 1
ReflectionResolution: 1.63→15.83 Å / Num. obs: 25539 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.028 / Net I/σ(I): 15.2
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.121 / % possible all: 89.5
Reflection
*PLUS
Rmerge(I) obs: 0.028

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MONOMER A FROM 5LYM PDB ENTRY (MONOCLINIC LYSOZYME)

5lym


Resolution: 1.63→15.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2526 9.9 %RANDOM
Rwork0.198 ---
obs0.198 25515 96.9 %-
Displacement parametersBiso mean: 16.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.63→15.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 9 136 2147
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.07
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.581.5
X-RAY DIFFRACTIONx_mcangle_it2.512
X-RAY DIFFRACTIONx_scbond_it2.82
X-RAY DIFFRACTIONx_scangle_it4.252.5
LS refinement shellResolution: 1.63→1.69 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 233 9.9 %
Rwork0.284 2124 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SCNTOPH19.SCN
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.284

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