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

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Basic information

Entry
Database: PDB / ID: 3guo
TitleT4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--phenol 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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 1.2Apr 9, 2014Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)37,7548
Polymers37,4192
Non-polymers3356
Water1,60389
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8794
Polymers18,7101
Non-polymers1703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8754
Polymers18,7101
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.514, 49.514, 130.253
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:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLY1AA1 - 121 - 12
21METMETGLYGLY1BB1 - 121 - 12
12LEULEUTHRTHR4AA13 - 2613 - 26
22LEULEUTHRTHR4BB13 - 2613 - 26
13ILEILEPROPRO1AA27 - 3727 - 37
23ILEILEPROPRO1BB27 - 3727 - 37
14ASPASPILEILE4AA38 - 5038 - 50
24ASPASPILEILE4BB38 - 5038 - 50
15GLYGLYHOHHOH1A - BA - J51 - 60251
25GLYGLYHOHHOH1BB - J51 - 60251

NCS ensembles :
ID
1
2
3
4
5

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Components

#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
#2: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
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: 2.16→46.28 Å / Num. obs: 16884 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 42.8
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 5.7 / % possible all: 99.9

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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: 2.16→46.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 18.617 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27248 848 5.1 %RANDOM
Rwork0.21383 ---
obs0.21666 15928 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.939 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.16→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 18 89 2693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222704
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9633644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52423.077130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97415500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4711530
X-RAY DIFFRACTIONr_chiral_restr0.1160.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022042
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21229
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21830
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0270.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.51698
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22522626
X-RAY DIFFRACTIONr_scbond_it2.25131173
X-RAY DIFFRACTIONr_scangle_it3.4014.51016
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
1100tight positional0.030.05
379tight positional0.030.05
5931tight positional0.030.05
2123medium positional0.170.5
496medium positional0.180.5
1100tight thermal0.110.5
379tight thermal0.110.5
5931tight thermal0.090.5
2123medium thermal0.642
496medium thermal0.362
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 55 -
Rwork0.253 1186 -
obs--99.92 %
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)
110.17621.47514.95114.38757.848216.2547-0.0049-0.22570.6524-0.4398-0.45490.1868-0.6198-1.49460.4598-0.1515-0.0166-0.0794-0.0231-0.0115-0.0983-0.79413.186-4.808
26.73991.5676-1.80687.8803-5.89724.47560.0049-0.3582-0.23310.0234-0.08250.72850.1367-0.27190.0776-0.2078-0.00250.01540.0388-0.1482-0.075-5.57511.56313.107
32.86080.10621.06812.41332.65018.29820.1337-0.1424-0.15740.2375-0.14170.05480.9897-0.63460.0081-0.0272-0.136-0.0216-0.14680.0315-0.16324.164.002-2.175
40.01830.0401-0.13450.2356-0.20991.0377-0.0137-0.04260.0269-0.0520.0920.0586-0.0249-0.1005-0.0783-0.0082-0.0107-0.0324-0.0048-0.0193-0.01589.76214.32-4.803
53.561.31857.913712.4388.081919.8119-0.4719-0.6260.1392-0.3535-0.13480.8166-1.7785-0.73540.60670.0321-0.0403-0.0122-0.1301-0.0676-0.09911.43525.397-6.873
619.347-3.3381-0.82638.48942.823817.4509-0.95161.38352.6365-0.53750.3729-0.6624-2.90762.00060.57870.4655-0.3901-0.2235-0.16380.24360.149412.97430.494-25.323
72.5737-0.24032.5492.93831.02498.2495-0.15450.24060.0836-0.14730.131-0.1702-0.77641.16730.0236-0.1152-0.17120.03230.0031-0.0219-0.161420.80420.68-10.264
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 DIFFRACTION3A501
5X-RAY DIFFRACTION3A601
6X-RAY DIFFRACTION4B170 - 675
7X-RAY DIFFRACTION4A165 - 166
8X-RAY DIFFRACTION4B165 - 166
9X-RAY DIFFRACTION5B1 - 12
10X-RAY DIFFRACTION6B13 - 50
11X-RAY DIFFRACTION7B51 - 162

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