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- PDB-1jsf: FULL-MATRIX LEAST-SQUARES REFINEMENT OF HUMAN LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1jsf
TitleFULL-MATRIX LEAST-SQUARES REFINEMENT OF HUMAN LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / HUMAN LYSOZYME / ENZYME
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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
NITRATE ION / Lysozyme C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHarata, K. / Abe, Y. / Muraki, M.
CitationJournal: Proteins / Year: 1998
Title: Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion.
Authors: Harata, K. / Abe, Y. / Muraki, M.
History
DepositionJan 5, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 10, 2021Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / struct_conn / struct_conn_type / struct_site
Item: _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id ..._pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,1558
Polymers14,7211
Non-polymers4347
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.050, 60.960, 32.960
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


Mass: 14720.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLACENTA / References: UniProt: P61626, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.94 Å3/Da / Density % sol: 36.5 %
Crystal growpH: 4.5
Details: 3M AMMONIUM NITRATE SOLUTION WITH PH 4.5 ACETATE BUFFER AND 2% PROTEIN, VAPOR DIFFUSION OVER 5M AMMONIUM NITRATE AT ROOM TEMPERATURE.
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 Mammonium nitrate11
22 %protein11
35 Mammonium nitrate12

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Jan 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.14→25.1 Å / Num. obs: 39326 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 6.2
Reflection shellResolution: 1.14→1.16 Å / Rmerge(I) obs: 0.267 / % possible all: 43.8

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Processing

Software
NameClassification
MADNESdata collection
MERGEFdata reduction
SHELXL-93model building
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
MADNESdata reduction
MERGEFdata scaling
SHELXL-93phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1REX

1rex


Resolution: 1.15→25.9 Å / Num. parameters: 11279 / Num. restraintsaints: 13436 / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.157 -10 %
all0.115 39270 -
obs0.112 -92.1 %
Solvent computationSolvent model: SWAT
Refine analyzeNum. disordered residues: 6
Refinement stepCycle: LAST / Resolution: 1.15→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 28 164 1253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.197
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.112
Solvent computation
*PLUS
Displacement parameters
*PLUS

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