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- PDB-207l: MUTANT HUMAN LYSOZYME C77A -

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Basic information

Entry
Database: PDB / ID: 207l
TitleMUTANT HUMAN LYSOZYME C77A
ComponentsLYSOZYME
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE (O-GLYCOSYL)-CYS) / MUTANT HUMAN LYSOZYME / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen ...metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Lysozyme C / 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 C / 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
N-ACETYL-L-CYSTEINE / Lysozyme C / Lysozyme C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatsushima, M. / Song, H.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1996
Title: A role of PDI in the reductive cleavage of mixed disulfides.
Authors: Nakamura, S. / Matsushima, M. / Song, H. / Kikuchi, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of a Glutathionylated Human Lysozyme: A Folding Intermediate Mimic in the Formation of a Disulfide Bond
Authors: Inaka, K. / Miki, K. / Kikuchi, M. / Taniyama, Y. / Matsushima, M.
#2: Journal: FEBS Lett. / Year: 1993
Title: Pdi and Glutathione-Mediated Reduction of the Glutathionylated Variant of Human Lysozyme
Authors: Hayano, T. / Inaka, K. / Otsu, M. / Taniyama, Y. / Miki, K. / Matsushima, M. / Kikuchi, M.
History
DepositionMar 26, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 30, 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: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8522
Polymers14,6891
Non-polymers1631
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.640, 60.700, 32.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LYSOZYME / HL_95ACC


Mass: 14688.627 Da / Num. of mol.: 1 / Mutation: C77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme
#2: Chemical ChemComp-SC2 / N-ACETYL-L-CYSTEINE / (2R)-2-acetamido-3-sulfanyl-propanoic acid


Type: peptide-like / Mass: 163.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3S
Details: C77 CHANGED TO ALA AND A CYSTEINE WAS CHEMICALLY BOUND ON THE SH GROUP OF CYS95 THROUGH A DISULFIDE BOND
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Description: INDEPENDENTLY REREFINED HUMAN LYSOZYME AT 1.5 A RESOLUTION BY PROLSQ
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120.0 mg/mlprotein1drop
21.8 M1dropNaCl
330 mMsodium phosphate1drop
42.0 M1reservoirNaCl
530 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 1, 1993 / Details: MIRROR-MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. obs: 8903 / % possible obs: 75.3 % / Observed criterion σ(I): 2 / Redundancy: 2.68 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.75→1.78 Å / % possible all: 42.2
Reflection shell
*PLUS
% possible obs: 42.2 %

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Processing

Software
NameClassification
WELMSdata collection
PROTEINdata reduction
PROTEINmodel building
PROLSQrefinement
WELMSdata reduction
PROTEINdata scaling
PROTEINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE HUMAN LYSOZYME

Resolution: 1.8→6 Å / σ(F): 0 /
Num. reflection% reflection
all8168 -
obs8168 78.6 %
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 10 123 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0360.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0661.5
X-RAY DIFFRACTIONp_mcangle_it1.5062
X-RAY DIFFRACTIONp_scbond_it1.9362
X-RAY DIFFRACTIONp_scangle_it2.7682.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1610.3
X-RAY DIFFRACTIONp_multtor_nbd0.1570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2020.3
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor17.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2115
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS

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