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- PDB-4evx: Crystal structure of putative phage endolysin from S. enterica -

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Basic information

Entry
Database: PDB / ID: 4evx
TitleCrystal structure of putative phage endolysin from S. enterica
ComponentsPutative phage endolysin
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Program for the Characterization of Secreted Effector Proteins / PCSEP / Midwest Center for Structural Genomics / MCSG / methylation
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #240 / : / Rna Polymerase Sigma Factor; Chain: A / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMichalska, K. / Li, H. / Jedrzejczak, R. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. / Program for the Characterization of Secreted Effector Proteins (PCSEP) / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative phage endolysin from S. enterica
Authors: Michalska, K. / Jedrzejczak, R. / Li, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. / Program for the Characterization of Secreted Effector ...Authors: Michalska, K. / Jedrzejczak, R. / Li, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. / Program for the Characterization of Secreted Effector Proteins (PCSEP) / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phage endolysin
B: Putative phage endolysin


Theoretical massNumber of molelcules
Total (without water)24,5212
Polymers24,5212
Non-polymers00
Water1,72996
1
A: Putative phage endolysin
B: Putative phage endolysin

A: Putative phage endolysin
B: Putative phage endolysin


Theoretical massNumber of molelcules
Total (without water)49,0424
Polymers49,0424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area7740 Å2
ΔGint-84 kcal/mol
Surface area18970 Å2
MethodPISA
2
A: Putative phage endolysin
B: Putative phage endolysin

A: Putative phage endolysin
B: Putative phage endolysin


Theoretical massNumber of molelcules
Total (without water)49,0424
Polymers49,0424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6410 Å2
ΔGint-48 kcal/mol
Surface area20290 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-21 kcal/mol
Surface area11470 Å2
MethodPISA
4
A: Putative phage endolysin

B: Putative phage endolysin


Theoretical massNumber of molelcules
Total (without water)24,5212
Polymers24,5212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area1870 Å2
ΔGint-20 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.400, 54.400, 261.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

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Components

#1: Protein Putative phage endolysin


Mass: 12260.509 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM3605 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic / References: UniProt: Q8ZLC6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.14 M CaCl2, 0.07 M Na acetate/HCl, 14% 2-propanol, 30% glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792914 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. all: 26515 / Num. obs: 26172 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.43 / Num. unique all: 1263 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→20.07 Å / Cor.coef. Fo:Fc: 0.9481 / Cor.coef. Fo:Fc free: 0.9396 / SU R Cruickshank DPI: 0.12 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
Details: hydrogen atoms have been added at the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1314 5.04 %RANDOM
Rwork0.1949 ---
all0.1959 26081 --
obs0.1959 26081 98.72 %-
Displacement parametersBiso mean: 40.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.4317 Å20 Å20 Å2
2---1.4317 Å20 Å2
3---2.8633 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 1.7→20.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 0 96 1666
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0143236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.25814HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1043SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes472HARMONIC5
X-RAY DIFFRACTIONt_it3208HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_chiral_improper_torsion213SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3770SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.77 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2465 135 4.78 %
Rwork0.2118 2690 -
all0.2134 2825 -
obs-2825 98.72 %
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)
11.90140.93170.24260.44683.28763.3728-0.13130.34240.0181-0.19080.1052-0.13330.23450.04910.02610.04430.034-0.0006-0.0022-0.0216-0.05279.8517-8.00677.3723
2-0.25980.09432.33331.93481.6931.6902-0.10040.1246-0.287-0.18280.39790.10050.5482-0.2554-0.29750.1342-0.1446-0.058-0.04980.0232-0.127-0.4964-15.77099.6091
31.4637-0.1655-3.16853.4434-0.25422.0790.05470.07990.1802-0.03970.01680.470.2485-0.0439-0.0715-0.0288-0.2154-0.0750.01630.0761-0.0625-15.8298-10.34956.3872
47.11060.7742-0.72262.36872.14620.72270.19690.15510.0625-0.2766-0.06250.27270.1138-0.4442-0.13440.1014-0.1281-0.08660.02060.0543-0.1107-9.7723-9.9736-0.4645
52.64462.04761.70696.91612.11054.03530.16890.0007-0.0064-0.0322-0.0810.10230.4689-0.1594-0.0880.0377-0.0299-0.0364-0.09780.0121-0.11241.0284-8.3191.3662
68.3876-0.6070.35522.36720.90712.37290.18080.0810.726-0.4051-0.0987-0.2093-0.0530.1104-0.0821-0.02310.00610.0415-0.1161-0.023-0.00728.50546.328111.4541
75.2489-0.7833-0.88263.63630.25277.16360.01290.15670.07170.01510.09880.12690.0144-0.4485-0.11170.01530.0169-0.0207-0.06350.0189-0.04461.7235-2.846814.4808
8-1.20780.66940.77581.32540.62670.5165-0.0182-0.077-0.06710.02080.0751-0.05770.01060.1267-0.05690.0814-0.1952-0.0728-0.04410.06680.0261-8.2024-19.920217.9291
9-0.57092.5808-1.39723.1703-1.54717.40130.1070.07750.2901-0.1612-0.05250.1657-0.3288-0.519-0.05450.05150.17030.0367-0.0730.0431-0.0476-2.665418.12723.289
101.82941.0559-1.21720.6094-0.49490-0.11380.16750.04750.0579-0.1319-0.1196-0.43220.2870.24570.1563-0.07780.0482-0.10480.0331-0.033912.428527.071915.3071
112.8196-0.81910.9593-1.88572.83752.7831-0.05470.008-0.25960.04940.1029-0.3358-0.3770.3608-0.04820.0695-0.09690.0892-0.10650.02060.098314.121920.180215.3109
128.5222-1.06833.92393.0345-1.09520.5429-0.24670.0753-0.39230.10420.1821-0.3655-0.3901-0.15540.06470.0973-0.0120.1094-0.1847-0.007-0.03066.525921.0812.5963
130.73361.7795-1.02495.4002-3.95243.8239-0.07450.1496-0.05320.1294-0.01210.0378-0.213-0.02070.08660.1284-0.2533-0.09350.070.07530.01017.734128.92117.2204
141.74451.84671.35356.33341.32324.69080.03260.03270.0674-0.05150.0389-0.0651-0.4128-0.3735-0.07150.04070.0740.0645-0.07040.0038-0.0559-3.771714.591612.9449
152.9771-0.7772-0.41374.41490.31975.1997-0.04180.2706-0.1355-0.32620.14570.1579-0.0224-0.6414-0.1039-0.00510.0168-0.00340.00790.0261-0.1087-4.72156.917120.046
161.25180.1193-0.405-0.2311-0.54710.2325-0.0314-0.03970.06910.0881-0.0086-0.0965-0.07460.09290.040.1393-0.03130.06430.00070.07610.079610.358718.444222.2338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|7 - A|14}A7 - 14
2X-RAY DIFFRACTION2{A|15 - A|25}A15 - 25
3X-RAY DIFFRACTION3{A|26 - A|35}A26 - 35
4X-RAY DIFFRACTION4{A|36 - A|50}A36 - 50
5X-RAY DIFFRACTION5{A|51 - A|69}A51 - 69
6X-RAY DIFFRACTION6{A|70 - A|82}A70 - 82
7X-RAY DIFFRACTION7{A|83 - A|97}A83 - 97
8X-RAY DIFFRACTION8{A|98 - A|103}A98 - 103
9X-RAY DIFFRACTION9{B|7 - B|23}B7 - 23
10X-RAY DIFFRACTION10{B|24 - B|28}B24 - 28
11X-RAY DIFFRACTION11{B|29 - B|36}B29 - 36
12X-RAY DIFFRACTION12{B|37 - B|43}B37 - 43
13X-RAY DIFFRACTION13{B|44 - B|50}B44 - 50
14X-RAY DIFFRACTION14{B|51 - B|78}B51 - 78
15X-RAY DIFFRACTION15{B|79 - B|95}B79 - 95
16X-RAY DIFFRACTION16{B|96 - B|100}B96 - 100

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