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- PDB-1swy: Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab ... -

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Basic information

Entry
Database: PDB / ID: 1swy
TitleUse of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure Determination
ComponentsLysozyme
KeywordsHYDROLASE / Rb+ binding sites / Ab initio direct methods
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / RUBIDIUM ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.06 Å
AuthorsMooers, B.H.M. / Matthews, B.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods.
Authors: Mooers, B.H. / Matthews, B.W.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)19,35113
Polymers18,5901
Non-polymers76112
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.199, 60.199, 95.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lysozyme / Lysis protein / Muramidase / Endolysin


Mass: 18590.377 Da / Num. of mol.: 1 / Mutation: D72A, R96E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Plasmid: PH1403 / Cell line (production host): RR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Rb
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.68 Å3/Da / Density % sol: 53.72 %
Description: SOLUTION WAS OBTAINED VERY QUICKLY. BIJVOET Patterson was easy to interpret.
Crystal growTemperature: 277 K / pH: 6.7
Details: sodium:potassium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.773 Å / Relative weight: 1
ReflectionResolution: 1.06→22 Å / Num. obs: 87349 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 7.4
Reflection shellResolution: 1.06→1.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4 / % possible all: 91.4

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
SHELXDphasing
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.06→22 Å / Num. parameters: 15912 / Num. restraintsaints: 18212 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ATOMS NOT IN 1 SIGMA ELECTRON DENSITY WERE REMOVED FROM THE MODEL. RESIDUES 55 AND 162-164 WERE DIFFICULT TO MODEL DUE TO DISORDER. NOT ALL OF THE DENISTY AROUND THE DISORDERED BME COULD BE MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.147 4321 5 %RANDOM
all0.123 87349 --
obs0.123 -96.3 %-
Solvent computationSolvent model: SHELXL IMPLEMENTATION OF BABINET METHOD SWAT 1 0.87379 SWAT 2 3.03190
Refine analyzeNum. disordered residues: 13
Refinement stepCycle: LAST / Resolution: 1.06→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 20 334 1766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.349
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.029
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.096

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