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- PDB-3hc7: Crystal structure of lysin B from Mycobacteriophage D29 -

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Basic information

Entry
Database: PDB / ID: 3hc7
TitleCrystal structure of lysin B from Mycobacteriophage D29
ComponentsGene 12 protein
KeywordsCELL ADHESION / alpha/beta sandwich
Function / homology
Function and homology information


cytolysis / metabolic process / viral release from host cell by cytolysis / Hydrolases; Acting on ester bonds / hydrolase activity / defense response to bacterium
Similarity search - Function
Lysin B, C-terminal linker domain / Lysin B, C-terminal linker domain / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Lysin B, C-terminal linker domain / Lysin B, C-terminal linker domain / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium phage D29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsSun, Q. / Sacchettini, J.C.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase
Authors: Payne, K. / Sun, Q. / Sacchettini, J. / Hatfull, G.F.
History
DepositionMay 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2016Group: Refinement description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gene 12 protein


Theoretical massNumber of molelcules
Total (without water)28,5471
Polymers28,5471
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.530, 92.530, 69.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

21A-2028-

HOH

31A-2030-

HOH

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Components

#1: Protein Gene 12 protein / Gp12


Mass: 28546.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium phage D29 (virus) / Gene: 12, gp12 / Plasmid: pLAM3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O64205
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 290 K / pH: 8
Details: 50mM Tris pH8, 20% PEG1000, 100mM Calcium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2009
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21027 / % possible obs: 99.8 %
Reflection shellResolution: 2→2.07 Å / % possible all: 99.5

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→41.38 Å / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.25 1978 10 %
Rwork0.205 --
obs-19777 94.8 %
Solvent computationBsol: 82.08 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 53.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.512 Å2-0 Å20 Å2
2---1.512 Å20 Å2
3---3.024 Å2
Refinement stepCycle: LAST / Resolution: 2→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 0 121 2094
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.635
X-RAY DIFFRACTIONf_dihedral_angle_d9.597
X-RAY DIFFRACTIONf_chiral_restr0.051
X-RAY DIFFRACTIONf_plane_restr0.003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.023000.26273X-RAY DIFFRACTION13
2.023-2.043000.267202X-RAY DIFFRACTION35
2.043-2.063000.291436X-RAY DIFFRACTION77
2.063-2.085000.299485X-RAY DIFFRACTION89
2.085-2.107000.3522X-RAY DIFFRACTION89
2.107-2.13000.277494X-RAY DIFFRACTION89
2.13-2.154000.26509X-RAY DIFFRACTION89
2.154-2.179000.268516X-RAY DIFFRACTION89
2.179-2.206000.244503X-RAY DIFFRACTION89
2.206-2.234000.272483X-RAY DIFFRACTION87
2.234-2.263000.29512X-RAY DIFFRACTION89
2.263-2.294000.273482X-RAY DIFFRACTION85
2.294-2.327000.244519X-RAY DIFFRACTION89
2.327-2.362000.231507X-RAY DIFFRACTION89
2.362-2.399000.215511X-RAY DIFFRACTION90
2.399-2.438000.22501X-RAY DIFFRACTION90
2.438-2.48000.21522X-RAY DIFFRACTION89
2.48-2.525000.205511X-RAY DIFFRACTION90
2.525-2.574000.207527X-RAY DIFFRACTION89
2.574-2.626000.193497X-RAY DIFFRACTION89
2.626-2.683000.194513X-RAY DIFFRACTION90
2.683-2.746000.208521X-RAY DIFFRACTION89
2.746-2.814000.203514X-RAY DIFFRACTION90
2.814-2.89000.206524X-RAY DIFFRACTION90
2.89-2.975000.191521X-RAY DIFFRACTION90
2.975-3.071000.188513X-RAY DIFFRACTION90
3.071-3.181000.199529X-RAY DIFFRACTION90
3.181-3.308000.173534X-RAY DIFFRACTION90
3.308-3.459000.196514X-RAY DIFFRACTION90
3.459-3.641000.175528X-RAY DIFFRACTION90
3.641-3.869000.154536X-RAY DIFFRACTION90
3.869-4.167000.158524X-RAY DIFFRACTION90
4.167-4.586000.152537X-RAY DIFFRACTION90
4.586-5.247000.177551X-RAY DIFFRACTION90
5.247-6.604000.21549X-RAY DIFFRACTION90
6.604-35.578000.226579X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 33.508 Å / Origin y: 18.9103 Å / Origin z: 22.0644 Å
111213212223313233
T0.4638 Å20.1943 Å2-0.0104 Å2-0.2726 Å20.0065 Å2--0.129 Å2
L2.1864 °2-2.156 °2-0.5771 °2-3.7345 °21.0531 °2--0.7645 °2
S0.6922 Å °0.5277 Å °-0.0389 Å °-1.0313 Å °-0.6163 Å °-0.0235 Å °-0.2592 Å °-0.2555 Å °-0.0696 Å °
Refinement TLS groupSelection details: chain A

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