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- PDB-3dke: Polar and non-polar cavities in phage T4 lysozyme -

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Basic information

Entry
Database: PDB / ID: 3dke
TitlePolar and non-polar cavities in phage T4 lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / T4 lysozyme / cavity / experimental phases / 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
AZIDE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / : / Endolysin
Similarity search - Component
Biological speciesBacteriophage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsLiu, L.J. / Matthews, B.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Use of experimental crystallographic phases to examine the hydration of polar and nonpolar cavities in T4 lysozyme
Authors: Liu, L. / Quillin, M.L. / Matthews, B.W.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_struct_conn_angle / 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 / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_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
X: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,79512
Polymers18,7561
Non-polymers1,03911
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.226, 60.226, 96.677
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules X

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


Mass: 18755.826 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L99A, M102L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage T4 (virus) / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme

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Non-polymers , 8 types, 267 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.0-2.2 M NaH2PO4 and K2HPO4, pH 6.9, 5mM BME, 5mM oxidized BME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796,0.9797,0.9742,0.9807
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97971
30.97421
40.98071
ReflectionResolution: 1.25→52.2 Å / Num. obs: 56299 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 23.2
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 13.9 / Num. unique all: 2753 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.25→52.13 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.915 / SU ML: 0.019 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17281 2851 5.1 %RANDOM
Rwork0.15538 ---
obs0.15626 53423 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.834 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.25→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 57 256 1618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9791883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5515172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9923.59464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.72915255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.381513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2722
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2974
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0520.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6711.5831
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15221337
X-RAY DIFFRACTIONr_scbond_it2.3933580
X-RAY DIFFRACTIONr_scangle_it3.4144.5543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 209 -
Rwork0.169 3840 -
obs--98.42 %
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)
11.0863-0.1290.7581.0631.62343.3799-0.0217-0.1132-0.01890.19480.0917-0.08920.0380.1214-0.070.0038-0.00410.0049-0.0098-0.0007-0.04441.6865.87411.312
20.95760.1512-0.36431.00370.1171.63090.0124-0.02880.05520.05340.02960.0246-0.10420.0611-0.0420.0109-0.00470.007-0.0096-0.0103-0.045739.92221.43121.561
35.40230.87521.80871.73310.88383.0208-0.0284-0.0484-0.03990.04510.00730.0580.0557-0.02470.02120.02260.0050.0145-0.01820.0003-0.041635.8628.49720.977
49.41721.85736.80782.63162.20511.4978-0.1344-0.45530.08820.0098-0.07360.1425-0.2209-0.68510.2081-0.01570.00260.01420.0275-0.0174-0.023421.8146.23112.002
51.45160.90280.66791.65680.96140.7040.0509-0.0956-0.03240.0579-0.03460.01550.0192-0.0529-0.01630.013-0.0102-0.0011-0.00110.0086-0.034829.2483.266.105
61.33170.1111.03621.63671.35352.277-0.0587-0.10460.08250.1017-0.02880.2744-0.0165-0.17730.08740.0141-0.01190.0163-0.00420.0195-0.030224.38610.5360.569
70.52610.33020.34370.69590.04580.5496-0.02360.0506-0.0136-0.09720.032-0.0197-0.01960.0153-0.00840.0167-0.0224-0.0024-0.0012-0.0001-0.035234.4510.389-3.574
83.87980.5821.5567.87530.99942.61940.05860.1075-0.2443-0.12890.1023-0.25140.11670.2142-0.1609-0.0098-0.00710.0071-0.015-0.017-0.039441.2980.5080.061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA1 - 121 - 12
2X-RAY DIFFRACTION2XA13 - 6213 - 62
3X-RAY DIFFRACTION3XA63 - 7363 - 73
4X-RAY DIFFRACTION4XA74 - 8474 - 84
5X-RAY DIFFRACTION5XA85 - 10585 - 105
6X-RAY DIFFRACTION6XA106 - 123106 - 123
7X-RAY DIFFRACTION7XA124 - 153124 - 153
8X-RAY DIFFRACTION8XA154 - 164154 - 164

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