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- PDB-4acv: Listeria monocytogenes Antigen B -

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Basic information

Entry
Database: PDB / ID: 4acv
TitleListeria monocytogenes Antigen B
Components(PROPHAGE LAMBDALM01, ANTIGEN B) x 2
KeywordsIMMUNE SYSTEM / SURFACE / PHAGE-RELATED
Function / homologyPutative tail termination protein / STM4215-like - #30 / STM4215-like / : / 2-Layer Sandwich / Alpha Beta / Prophage LambdaLm01, antigen B / Prophage LambdaLm01, antigen B
Function and homology information
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.401 Å
AuthorsHuyet, J. / Naylor, C.E. / Geddes, S. / Basak, A.K.
CitationJournal: To be Published
Title: Structure of Listeria Monocytogenes Antigen B Reveals its Relationship to Phage Tail Proteins
Authors: Huyet, J. / Naylor, C.E. / Geddes, S. / Basak, A.K.
History
DepositionDec 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROPHAGE LAMBDALM01, ANTIGEN B
B: PROPHAGE LAMBDALM01, ANTIGEN B


Theoretical massNumber of molelcules
Total (without water)29,9382
Polymers29,9382
Non-polymers00
Water1,78399
1
A: PROPHAGE LAMBDALM01, ANTIGEN B
B: PROPHAGE LAMBDALM01, ANTIGEN B

A: PROPHAGE LAMBDALM01, ANTIGEN B
B: PROPHAGE LAMBDALM01, ANTIGEN B

A: PROPHAGE LAMBDALM01, ANTIGEN B
B: PROPHAGE LAMBDALM01, ANTIGEN B


Theoretical massNumber of molelcules
Total (without water)89,8146
Polymers89,8146
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area10270 Å2
ΔGint-74.2 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.456, 122.456, 122.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 48:48 )
211CHAIN B AND (RESSEQ 48:53 )

NCS oper: (Code: given
Matrix: (0.65004, 0.68173, -0.33569), (-0.36854, 0.66916, 0.64529), (0.66455, -0.29575, 0.68623)
Vector: -0.1522, 2.16274, -2.06562)

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Components

#1: Protein PROPHAGE LAMBDALM01, ANTIGEN B / ANTIGEN B


Mass: 14968.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: 10403S / Variant: SEROVAR 1/2A / Plasmid: PET151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G2K1X0, UniProt: A0A0H3G917*PLUS
#2: Protein PROPHAGE LAMBDALM01, ANTIGEN B / ANTIGEN B


Mass: 14969.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: 10403S / Variant: SEROVAR 1/2A / Plasmid: PET151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G2K1X0, UniProt: A0A0H3G917*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXPRESSED PROTEIN HAD HIS-TAG WHICH WAS REMOVED.

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8 / Details: 4M NA FORMATE, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332, 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 1, 2008 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.97921
ReflectionResolution: 2.4→86.59 Å / Num. obs: 12093 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 30.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 22.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 8.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.401→38.724 Å / SU ML: 0.35 / σ(F): 1.98 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 577 4.8 %
Rwork0.1855 --
obs0.1878 12085 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.622 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.401→38.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 99 1948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071874
X-RAY DIFFRACTIONf_angle_d0.9962530
X-RAY DIFFRACTIONf_dihedral_angle_d16.335667
X-RAY DIFFRACTIONf_chiral_restr0.06302
X-RAY DIFFRACTIONf_plane_restr0.003318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5X-RAY DIFFRACTIONPOSITIONAL
12B5X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4006-2.64220.2761610.19352811X-RAY DIFFRACTION100
2.6422-3.02440.28181270.19072866X-RAY DIFFRACTION100
3.0244-3.80990.25011530.17812874X-RAY DIFFRACTION100
3.8099-38.72910.18921360.17432957X-RAY DIFFRACTION100
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)
13.4479-0.8474-0.3830.22330.1331.20730.28180.37710.4036-0.298-0.1402-0.3274-0.14720.0382-0.13920.23350.01580.08960.16910.04650.22948.235250.654418.659
20.7286-0.3387-0.79541.3039-0.65922.1236-0.0706-0.1388-0.0262-0.1024-0.132-0.34510.17560.23140.17910.1721-0.02790.05060.1920.00650.228458.772929.799827.7692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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