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- PDB-4ekp: T4 Lysozyme L99A/M102H with Nitrobenzene Bound -

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Basic information

Entry
Database: PDB / ID: 4ekp
TitleT4 Lysozyme L99A/M102H with Nitrobenzene 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / NITROBENZENE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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)44,17917
Polymers42,8092
Non-polymers1,37015
Water6,053336
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0909
Polymers21,4041
Non-polymers6868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0898
Polymers21,4041
Non-polymers6857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,17917
Polymers42,8092
Non-polymers1,37015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2100 Å2
ΔGint-13 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.370, 75.530, 52.720
Angle α, β, γ (deg.)90.000, 93.220, 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, 351 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-NBZ / NITROBENZENE


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 59.044 Da / Num. of mol.: 3 / 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


Mass: 18.015 Da / Num. of mol.: 336 / 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: 1.64→50 Å / Num. obs: 45872 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.456 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.64-1.730.3353167046794199.1
1.73-1.840.2254.37162606575199.1
1.84-1.970.1556.32148155980199
1.97-2.120.09210.4130735257199.2
2.12-2.320.06115.13125375024199.1
2.32-2.590.04220.45113994571199.2
2.59-2.990.03325.88102084088198.6
2.99-3.670.02435.2985793456197.8
3.67-5.190.01745.8166812660198.2
5.19-100.01745.9332301265197.4
10-500.01352.79501202191.8

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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: 1.64→43.185 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8955 / SU ML: 0.39 / σ(F): 1.99 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 1839 4.01 %RANDOM
Rwork0.1694 ---
obs0.1705 45871 98.83 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.123 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 55.61 Å2 / Biso mean: 17.5469 Å2 / Biso min: 2.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.7828 Å20 Å2-1.4572 Å2
2---0.2784 Å20 Å2
3----0.5044 Å2
Refinement stepCycle: LAST / Resolution: 1.64→43.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 79 336 3163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083022
X-RAY DIFFRACTIONf_angle_d1.0574097
X-RAY DIFFRACTIONf_chiral_restr0.069447
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d12.7381141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.68440.30011440.2483399354399
1.6844-1.73390.2861410.22243376351799
1.7339-1.78990.23631390.20793377351699
1.7899-1.85390.21431440.18423372351699
1.8539-1.92810.19341390.1653387352699
1.9281-2.01580.19331440.1623384352899
2.0158-2.12210.20211420.15933372351499
2.1221-2.25510.18381400.15943384352499
2.2551-2.42920.20141420.15913415355799
2.4292-2.67360.21761380.16543388352699
2.6736-3.06040.191430.17233396353999
3.0604-3.85540.16161410.15723359350098
3.8554-43.19950.17631420.16193423356598
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)
10.68850.14420.19250.6257-0.04230.82890.0837-0.17410.20260.07830.00070.0876-0.158-0.05830.02750.02970.01520.02330.019-0.0210.01526.572213.746410.2622
20.3480.13810.06780.34940.13880.46690.0350.0242-0.0587-0.00710.0353-0.01410.1025-0.02260.0790.0306-0.0086-0.0060.02740.00650.027930.327220.2641-9.2728
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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