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- PDB-3gup: T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity... -

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Basic information

Entry
Database: PDB / ID: 3gup
TitleT4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine binding
ComponentsLysozyme
KeywordsHYDROLASE / T4 lysozyme / apolar cavity / buried charge / ligand binding / Antimicrobial / Bacteriolytic enzyme / Glycosidase
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 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
pyridine / CARBONATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLiu, L. / Matthews, B.W.
CitationJournal: Biochemistry / Year: 2009
Title: Use of stabilizing mutations to engineer a charged group within a ligand-binding hydrophobic cavity in T4 lysozyme.
Authors: Liu, L. / Baase, W.A. / Michael, M.M. / Matthews, B.W.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.4Sep 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
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,94312
Polymers37,4192
Non-polymers52310
Water4,558253
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0237
Polymers18,7101
Non-polymers3136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9205
Polymers18,7101
Non-polymers2104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.957, 48.957, 129.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 12
2111B1 - 12
1124A13 - 26
2124B13 - 26
1131A27 - 37
2131B27 - 37
1144A38 - 50
2144B38 - 50
1151A51 - 602
2151B - A51 - 604

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 18709.568 Da / Num. of mol.: 2 / Mutation: T21C/S38D/L99A/M102E/E108V/S117V/T142C/N144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: p1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-0PY / pyridine / Azabenzene / Azine / Pyridine


Mass: 79.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N
#3: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 8000, 0.14M magnesium/calcium sulfate, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007 / Details: Si(111)
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→48.96 Å / Num. obs: 47402 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 20
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GUI

3gui


Resolution: 1.5→48.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.527 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 2403 5.1 %RANDOM
Rwork0.21134 ---
obs0.21344 44992 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.654 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2--1.2 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 31 253 2870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222699
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9673634
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2915334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37123.178129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97915498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4071529
X-RAY DIFFRACTIONr_chiral_restr0.110.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022033
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21359
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21854
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2171.51687
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57922608
X-RAY DIFFRACTIONr_scbond_it2.6431182
X-RAY DIFFRACTIONr_scangle_it3.9334.51020
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
192tight positional0.020.05
379tight positional0.020.05
5912tight positional0.020.05
2123medium positional0.070.5
496medium positional0.060.5
192tight thermal0.170.5
379tight thermal0.110.5
5912tight thermal0.120.5
2123medium thermal0.432
496medium thermal0.342
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 165 -
Rwork0.252 3400 -
obs--99.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8512-0.2649-1.49173.3420.25584.67520.02660.2949-0.2226-0.0276-0.0942-0.06390.18390.75170.0676-0.09580.00280.02490.1297-0.0139-0.06980.768-13.49958.276
27.93331.41191.27676.4538-0.61634.33420.024-0.75320.11930.5905-0.3581-0.4308-0.39310.43140.3342-0.0975-0.0197-0.03610.24220.0536-0.03665.452-11.99376.69
32.3265-0.2006-0.16920.7173-0.47233.67150.016-0.1090.1341-0.0607-0.0148-0.0607-0.45840.4163-0.0012-0.0065-0.0460.0270.0177-0.0192-0.0673-3.965-4.16261.53
40.35440.07530.03760.6269-0.07551.65340.0025-0.0801-0.026-0.0824-0.0146-0.01870.01380.02090.012-0.00890.02540.00760.0045-0.0006-0.0503-9.397-14.02158.928
53.3847-0.3145-0.01853.7777-1.21426.717-0.0635-0.0527-0.09390.2601-0.0132-0.25950.75950.19710.07670.11070.0021-0.0127-0.0990.0272-0.065-11.006-25.37956.818
65.03121.5543-0.68468.08770.86544.2769-0.30640.492-0.3564-0.77650.02150.09710.3912-0.34680.28490.2153-0.01890.0484-0.0963-0.0288-0.0461-12.494-29.93738.404
70.7039-0.1063-0.46722.2555-0.17223.7082-0.0131-0.0642-0.059-0.10860.02050.1290.403-0.4465-0.00740.0147-0.0446-0.0189-0.00650.0281-0.0672-20.32-20.50853.575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2A13 - 50
3X-RAY DIFFRACTION3A51 - 162
4X-RAY DIFFRACTION4A170 - 735
5X-RAY DIFFRACTION4A165 - 169
6X-RAY DIFFRACTION4B165 - 167
7X-RAY DIFFRACTION4B168 - 732
8X-RAY DIFFRACTION5B1 - 12
9X-RAY DIFFRACTION6B13 - 50
10X-RAY DIFFRACTION7B51 - 162

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