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- PDB-3hua: 4,5,6,7-tetrahydroindole in complex with T4 lysozyme L99A/M102Q -

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Basic information

Entry
Database: PDB / ID: 3hua
Title4,5,6,7-tetrahydroindole in complex with T4 lysozyme L99A/M102Q
ComponentsLysozyme
KeywordsHYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / Antimicrobial
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 / 4,5,6,7-tetrahydro-1H-indole / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFMAC / Resolution: 1.4 Å
AuthorsBoyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.
Authors: Boyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K.
History
DepositionJun 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 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 1.4Sep 6, 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
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0195
Polymers18,6461
Non-polymers3724
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.327, 60.327, 97.438
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18646.316 Da / Num. of mol.: 1 / Mutation: S44D,L99A,M102Q,N144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Strain: Enterobacteria Phage T4 Sensu Lato / Gene: E / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-JZ9 / 4,5,6,7-tetrahydro-1H-indole


Mass: 121.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11589 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11589 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 40838 / Num. obs: 40838 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Χ2: 2.949 / Net I/σ(I): 53.728
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 4.88 / Num. unique all: 4019 / Χ2: 1.312 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: REFMAC
Starting model: PDB ENTRY 1LGU

1lgu


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.672 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2050 5 %RANDOM
Rwork0.173 ---
all0.174 40790 --
obs0.174 40790 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.57 Å2 / Biso mean: 15.49 Å2 / Biso min: 6.38 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: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 22 294 1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221526
X-RAY DIFFRACTIONr_angle_refined_deg1.141.962084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50723.54479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61115292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5821517
X-RAY DIFFRACTIONr_chiral_restr0.0760.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021182
X-RAY DIFFRACTIONr_nbd_refined0.1910.2727
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.237
X-RAY DIFFRACTIONr_mcbond_it0.6691.5929
X-RAY DIFFRACTIONr_mcangle_it1.01121468
X-RAY DIFFRACTIONr_scbond_it1.5163677
X-RAY DIFFRACTIONr_scangle_it2.0384.5597
X-RAY DIFFRACTIONr_rigid_bond_restr0.88731606
X-RAY DIFFRACTIONr_sphericity_free2.8463294
X-RAY DIFFRACTIONr_sphericity_bonded1.89331483
LS refinement shellResolution: 1.4→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 152 -
Rwork0.263 2748 -
all-2900 -
obs-2748 97.15 %

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