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- PDB-2ou0: 1-methylpyrrole in complex with T4 Lysozyme L99A -

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Basic information

Entry
Database: PDB / ID: 2ou0
Title1-methylpyrrole in complex with T4 Lysozyme L99A
ComponentsLysozyme
KeywordsHYDROLASE / PROTEIN-LIGAND COMPLEX / MODEL SYSTEM
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
1-METHYL-1H-PYRROLE / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGraves, A.P. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Predicting absolute ligand binding free energies to a simple model site.
Authors: Mobley, D.L. / Graves, A.P. / Chodera, J.D. / McReynolds, A.C. / Shoichet, B.K. / Dill, K.A.
History
DepositionFeb 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7115
Polymers18,3591
Non-polymers3524
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.205, 60.205, 96.372
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: 18359.023 Da / Num. of mol.: 1
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: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MR3 / 1-METHYL-1H-PYRROLE


Mass: 81.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 15355 / Num. obs: 15355 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.112 / Χ2: 1.008 / Net I/σ(I): 8.7
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.569 / Num. unique all: 1484 / Χ2: 1.014 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 181L

181l


Resolution: 1.94→52.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.592 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 749 5 %RANDOM
Rwork0.191 ---
all0.193 14992 --
obs0.193 14992 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.959 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.94→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 22 200 1515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221330
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9641794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9025164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92823.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89915239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0461513
X-RAY DIFFRACTIONr_chiral_restr0.070.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02996
X-RAY DIFFRACTIONr_nbd_refined0.1850.2677
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.225
X-RAY DIFFRACTIONr_mcbond_it0.6351.5840
X-RAY DIFFRACTIONr_mcangle_it0.7321291
X-RAY DIFFRACTIONr_scbond_it1.6673559
X-RAY DIFFRACTIONr_scangle_it2.1644.5501
LS refinement shellResolution: 1.942→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 51 -
Rwork0.289 984 -
obs-1035 94.52 %

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