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- PDB-4ekr: T4 Lysozyme L99A/M102H with 2-Cyanophenol Bound -

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Basic information

Entry
Database: PDB / ID: 4ekr
TitleT4 Lysozyme L99A/M102H with 2-Cyanophenol Bound
ComponentsLysozyme
KeywordsHYDROLASE / Alkylation of Cys97
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
2-hydroxybenzonitrile / ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMerski, M. / Shoichet, B.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Engineering a model protein cavity to catalyze the Kemp elimination.
Authors: Merski, M. / Shoichet, B.K.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)44,17517
Polymers42,8092
Non-polymers1,36615
Water5,549308
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2049
Polymers21,4041
Non-polymers8008
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9718
Polymers21,4041
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,17517
Polymers42,8092
Non-polymers1,36615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.170, 75.630, 52.800
Angle α, β, γ (deg.)90.000, 93.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 21404.426 Da / Num. of mol.: 2 / Mutation: T21C/S38D/L99A/M102H/E108V/S117V/T142C/N144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme

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Non-polymers , 6 types, 323 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-0R0 / 2-hydroxybenzonitrile / 2-Cyanophenol


Mass: 119.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5NO
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2010
RadiationMonochromator: two flat Si(111) crystals, mounted in a model DCM from Khozu
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 57470 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.49-1.570.3323.06220368557195.8
1.57-1.670.2274.38222198542195.9
1.67-1.780.1526.44190457256195.5
1.78-1.920.1079.2184256945194.8
1.92-2.110.06714.13178906677193.7
2.11-2.360.04621.11154045707192.4
2.36-2.720.03427.46133964901190.7
2.72-3.330.02832.39114404120188.7
3.33-4.710.0243.4789143117186.4
4.71-500.01846.4249541648182

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E97

4e97


Resolution: 1.49→48.095 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8873 / SU ML: 0.35 / σ(F): 1.99 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 2277 3.96 %RANDOM
Rwork0.1819 ---
obs0.1828 57470 93.12 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.508 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 51.29 Å2 / Biso mean: 15.4394 Å2 / Biso min: 3.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.4743 Å20 Å2-0.0187 Å2
2--2.4668 Å20 Å2
3----0.9924 Å2
Refinement stepCycle: LAST / Resolution: 1.49→48.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 83 308 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142968
X-RAY DIFFRACTIONf_angle_d1.4924013
X-RAY DIFFRACTIONf_chiral_restr0.093438
X-RAY DIFFRACTIONf_plane_restr0.008521
X-RAY DIFFRACTIONf_dihedral_angle_d12.7521104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.52240.29071510.25073521367296
1.5224-1.55780.27561480.2353565371396
1.5578-1.59680.2741450.2223564370996
1.5968-1.640.24661400.20533493363396
1.64-1.68820.22671520.19313522367495
1.6882-1.74270.21621480.18033548369696
1.7427-1.8050.22961460.17443505365195
1.805-1.87730.18821460.17353511365795
1.8773-1.96270.20961430.17823486362994
1.9627-2.06620.19991370.17153468360594
2.0662-2.19570.18541470.16873466361393
2.1957-2.36520.19271370.16643396353392
2.3652-2.60320.21321380.17913366350491
2.6032-2.97980.20421310.1863344347590
2.9798-3.7540.16721400.1683261340187
3.754-48.11970.19831280.18063177330584
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)
10.61630.17360.27050.4218-0.33380.56770.0115-0.13790.140.1047-0.00510.0879-0.1113-0.07970.1852-0.06140.02020.0725-0.0493-0.0279-0.05366.551713.74810.3681
20.47530.24250.11950.65470.28220.57660.01620.0441-0.0315-0.01990.0363-0.01630.05330.0046-0.01940.0561-0.0019-0.00310.04680.00270.056930.237520.4572-9.382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid -10:164A-10 - 164
2X-RAY DIFFRACTION2chain B and resid -9:164B-9 - 164

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