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- PDB-5bu8: HK620 Tail Needle crystallized at pH 7.5 and derivatized with Xenon -

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Basic information

Entry
Database: PDB / ID: 5bu8
TitleHK620 Tail Needle crystallized at pH 7.5 and derivatized with Xenon
Components(DNA stabilization protein) x 2
KeywordsVIRAL PROTEIN / HK620 / Tail Needle / Membrane penetration
Function / homology
Function and homology information


Helix Hairpins - #940 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
XENON / DNA stabilization protein
Similarity search - Component
Biological speciesSalmonella phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsSankhala, R.S. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100888 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.
Authors: Bhardwaj, A. / Sankhala, R.S. / Olia, A.S. / Brooke, D. / Casjens, S.R. / Taylor, D.J. / Prevelige, P.E. / Cingolani, G.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jun 17, 2020Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA stabilization protein
B: DNA stabilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94710
Polymers46,0792
Non-polymers8688
Water5,405300
1
A: DNA stabilization protein
hetero molecules

A: DNA stabilization protein
hetero molecules

A: DNA stabilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,67918
Polymers62,9833
Non-polymers1,69615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_1095x,y,z1
crystal symmetry operation3_6105x,y,z1
2
B: DNA stabilization protein
hetero molecules

B: DNA stabilization protein
hetero molecules

B: DNA stabilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,16212
Polymers75,2543
Non-polymers9089
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_1085x,y,z1
crystal symmetry operation3_7105x,y,z1
Unit cell
Length a, b, c (Å)43.642, 43.642, 271.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-301-

CA

21A-302-

XE

31A-303-

XE

41A-304-

XE

51A-305-

XE

61B-301-

CA

71B-302-

XE

81B-303-

XE

91A-461-

HOH

101B-521-

HOH

111B-562-

HOH

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Components

#1: Protein DNA stabilization protein


Mass: 20994.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage HK620 (virus) / Gene: 26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9AYZ3
#2: Protein DNA stabilization protein


Mass: 25084.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage HK620 (virus) / Gene: 26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9AYZ3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsResidues 26-46 in chain A had been modeled as a poly ALA but represented here as UNK residues in ...Residues 26-46 in chain A had been modeled as a poly ALA but represented here as UNK residues in the coordinates. Residue numbers are arbitrary as the exact registry is not clear. Full sequence is the same as that of the chain B.

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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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 1000, 0.1M Tris pH 7.5 derivatized with Xenon gas prior to data collection
PH range: 7.5

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 6, 2007
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→28.988 Å / Num. obs: 26538 / % possible obs: 90.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.11 / Net I/σ(I): 23.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 7.9 / % possible all: 58.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POH

2poh


Resolution: 2.202→28.988 Å / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 26.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1468 5.55 %Thin resolution shells
Rwork0.2263 ---
obs0.2306 26470 90.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→28.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 8 300 3113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062830
X-RAY DIFFRACTIONf_angle_d0.8923860
X-RAY DIFFRACTIONf_dihedral_angle_d14.578998
X-RAY DIFFRACTIONf_chiral_restr0.034487
X-RAY DIFFRACTIONf_plane_restr0.004502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2211-2.29880.3207880.28021633X-RAY DIFFRACTION58
2.2988-2.38870.30681100.25171883X-RAY DIFFRACTION69
2.3887-2.49460.25271320.24442272X-RAY DIFFRACTION81
2.4946-2.62220.26711530.24292582X-RAY DIFFRACTION92
2.6222-2.78060.23621500.23132636X-RAY DIFFRACTION94
2.7806-2.9860.26681300.20482646X-RAY DIFFRACTION95
2.986-3.26960.2691820.22692713X-RAY DIFFRACTION96
3.2696-3.70530.22131550.2082635X-RAY DIFFRACTION94
3.7053-4.53730.21791480.20152622X-RAY DIFFRACTION94
4.5373-8.29180.27332100.25632580X-RAY DIFFRACTION91
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)
10.1102-0.00910.05770.0321-0.18131.4861-0.0594-0.0580.07370.1103-0.08120.048-0.12510.1804-0.1650.18840.01080.01960.1033-0.00060.022722.1712113.851394.9698
20.2262-0.0476-0.04620.1406-0.080.773-0.02290.03090.0097-0.01620.0201-0.01730.0127-0.0779-0.00770.0682-0.01950.00360.053-0.00380.081223.1249111.4033191.1851
30.09430.0255-0.10180.04290.1381.0386-0.0716-0.05390.01950.0906-0.0431-0.0470.0216-0.0834-0.05760.16990.0413-0.00620.1484-0.03140.018843.3467100.1145-40.5535
40.1824-0.01240.07170.18550.01170.62810.0217-0.00160.0071-0.0505-0.00350.03860.07930.01590.00590.04240.0037-0.00360.05040.00020.05642.2344102.851755.6689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 233 )
3X-RAY DIFFRACTION3chain 'B' and (resid 56 through 139 )
4X-RAY DIFFRACTION4chain 'B' and (resid 140 through 233 )

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