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- PDB-5bu5: HK620 Tail Needle crystallized at pH 9 (crystal form I) -

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Basic information

Entry
Database: PDB / ID: 5bu5
TitleHK620 Tail Needle crystallized at pH 9 (crystal form I)
ComponentsDNA stabilization protein
KeywordsVIRAL PROTEIN / tail needle / viral genome-ejection / coiled-coil / trimer / bacteriophage
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
DNA stabilization protein
Similarity search - Component
Biological speciesEnterobacteria phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å
AuthorsBhardwaj, A. / Cingolani, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA56036 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
SupersessionJun 24, 2015ID: 4FMY
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Data collection / Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Jan 13, 2016Group: Database references
Revision 1.4Sep 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 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA stabilization protein
B: DNA stabilization protein
C: DNA stabilization protein
D: DNA stabilization protein
E: DNA stabilization protein
F: DNA stabilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,66010
Polymers150,5096
Non-polymers1514
Water16,682926
1
A: DNA stabilization protein
B: DNA stabilization protein
C: DNA stabilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3305
Polymers75,2543
Non-polymers762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23420 Å2
ΔGint-137 kcal/mol
Surface area23690 Å2
MethodPISA
2
D: DNA stabilization protein
E: DNA stabilization protein
F: DNA stabilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3305
Polymers75,2543
Non-polymers762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23440 Å2
ΔGint-134 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.032, 73.265, 77.355
Angle α, β, γ (deg.)96.64, 89.77, 111.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA stabilization protein


Mass: 25084.785 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK620 (virus) / Gene: 26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9AYZ3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 926 / 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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 40% PEG 4000, 0.1M potassium chloride, 0.1M TAPS buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2007
Details: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK. RH-COATED SI MIRROR FOR VERTICAL FOCUSING
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.95→15 Å / Num. obs: 72716 / % possible obs: 93.1 % / Redundancy: 1.8 % / Rsym value: 0.136 / Net I/σ(I): 14.45
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.54 / Rsym value: 0.41 / % possible all: 73.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C9I

3c9i


Resolution: 1.952→14.947 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 24.69 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 2011 2.95 %Random Selection
Rwork0.201 ---
obs0.2017 68211 87.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→14.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7920 0 4 926 8850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047992
X-RAY DIFFRACTIONf_angle_d0.88210890
X-RAY DIFFRACTIONf_dihedral_angle_d12.6492880
X-RAY DIFFRACTIONf_chiral_restr0.0341374
X-RAY DIFFRACTIONf_plane_restr0.0041410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9518-2.00050.3788890.31383136X-RAY DIFFRACTION58
2.0005-2.05450.33381330.28864487X-RAY DIFFRACTION82
2.0545-2.11480.37011420.30444635X-RAY DIFFRACTION86
2.1148-2.18290.28721490.24184975X-RAY DIFFRACTION91
2.1829-2.26060.27611440.23414702X-RAY DIFFRACTION88
2.2606-2.35080.26391370.22954631X-RAY DIFFRACTION85
2.3508-2.45740.27071440.22324599X-RAY DIFFRACTION85
2.4574-2.58630.25051410.21794626X-RAY DIFFRACTION86
2.5863-2.74740.19771480.21664714X-RAY DIFFRACTION87
2.7474-2.9580.24931390.20684748X-RAY DIFFRACTION87
2.958-3.25290.18441580.19635185X-RAY DIFFRACTION96
3.2529-3.71730.21041640.17095292X-RAY DIFFRACTION97
3.7173-4.65970.16031600.14685236X-RAY DIFFRACTION97
4.6597-14.94790.17291630.1725234X-RAY DIFFRACTION97
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)
10.11310.04590.04462.27912.18882.5519-0.06280.0208-0.02510.2405-0.09880.14830.3879-0.20320.18650.186-0.01150.00010.23180.00660.222614.7634-72.0912-76.4389
20.5409-0.18410.1321.46710.19391.4683-0.0929-0.07430.17020.21650.1318-0.12430.06130.093-0.07540.16230.0071-0.04260.1997-0.00310.2310.9583-20.22791.054
30.2525-0.3326-0.4320.59890.97311.8917-0.00080.0078-0.00580.15640.03990.03640.3140.034-0.16510.2704-0.0083-0.00930.19170.02930.244714.2375-67.4588-72.8235
41.1444-0.07590.06241.50570.07371.12180.06840.08680.1602-0.0728-0.0207-0.062-0.0670.1208-0.01110.24150.0228-0.01680.2444-0.00150.210213.9601-25.4822-15.367
51.03390.21650.14660.7322-0.46910.37990.018-0.13960.11480.40670.0681-0.2579-0.11030.1424-0.06130.2950.0591-0.1050.2558-0.07820.287116.4116-15.641713.1733
60.1737-0.1797-0.17861.80711.7962.2129-0.0771-0.012-0.0323-0.0732-0.07920.1826-0.0272-0.0840.1910.1867-0.03410.0320.17110.0140.252812.7915-70.8627-77.0413
70.4717-0.1872-0.09440.77760.07751.0833-0.061-0.02540.21410.15690.0783-0.1514-0.04840.13070.00390.21010.021-0.04850.2324-0.0250.276613.6444-17.4249-0.4272
80.0231-0.2359-0.25841.95331.9842.3965-0.0499-0.00980.0144-0.1857-0.13330.1542-0.227-0.15980.25240.17240.0049-0.00920.22120.00610.212141.608115.434-3.0505
90.5586-0.0012-0.17181.30410.3581.4345-0.07540.052-0.1024-0.19460.0921-0.07070.07390.0558-0.04790.2149-0.03610.03120.187-0.00290.22237.2373-36.4518-80.5231
100.18310.21780.27011.00911.55072.8207-0.007-0.00430.003-0.08620.04910.0409-0.17420.0572-0.08690.23860.0103-0.00480.1890.02240.219841.133510.7717-6.6502
113.56540.98820.04633.9840.20521.45120.0927-0.1114-0.22820.1688-0.0365-0.14810.10110.1761-0.04490.193-0.04240.02180.2409-0.01960.132740.5286-27.0119-61.9408
120.9387-0.2616-0.25171.3066-0.20980.69430.01430.1736-0.0951-0.30770.103-0.24940.32420.2545-0.05250.275-0.04140.07830.2335-0.03690.278242.2412-40.7324-89.1715
130.03110.20390.19021.36811.16421.4134-0.0611-0.0033-0.0017-0.0261-0.03190.1465-0.05030.00450.20510.1890.0286-0.05250.244-0.01350.260439.669314.173-2.4623
140.61190.18960.24430.95770.37891.20910.02330.0729-0.1751-0.1680.0534-0.23090.05570.1392-0.03450.2303-0.01660.04070.2333-0.01260.274739.9293-39.2693-79.0435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 233 )
3X-RAY DIFFRACTION3chain 'B' and (resid 60 through 147 )
4X-RAY DIFFRACTION4chain 'B' and (resid 148 through 175 )
5X-RAY DIFFRACTION5chain 'B' and (resid 176 through 233 )
6X-RAY DIFFRACTION6chain 'C' and (resid 60 through 139 )
7X-RAY DIFFRACTION7chain 'C' and (resid 140 through 233 )
8X-RAY DIFFRACTION8chain 'D' and (resid 60 through 139 )
9X-RAY DIFFRACTION9chain 'D' and (resid 140 through 233 )
10X-RAY DIFFRACTION10chain 'E' and (resid 60 through 147 )
11X-RAY DIFFRACTION11chain 'E' and (resid 148 through 165 )
12X-RAY DIFFRACTION12chain 'E' and (resid 166 through 233 )
13X-RAY DIFFRACTION13chain 'F' and (resid 60 through 139 )
14X-RAY DIFFRACTION14chain 'F' and (resid 140 through 233 )

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