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- PDB-2ob9: Structure of bacteriophage HK97 tail assembly chaperone -

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Basic information

Entry
Database: PDB / ID: 2ob9
TitleStructure of bacteriophage HK97 tail assembly chaperone
ComponentsTail assembly chaperone
KeywordsCHAPERONE / Bacteriophage HK97 / morphogenesis / tail assembly chaperone
Function / homology
Function and homology information


Phage tail assembly chaperone gp13-like / Minor tail T / Phage tail assembly chaperone Gp13-like / Tail assembly chaperone Gp13-like superfamily / Phage tail assembly chaperone / Minor tail protein T / rbstp2171 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gp14 / Tail assembly chaperone
Similarity search - Component
Biological speciesEnterobacteria phage HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMcGrath, T.E. / Tuite, A. / Bona, D. / Saridakis, V. / Edwards, A.M. / Maxwell, K. / Chirgadze, N.Y.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: A conserved spiral structure for highly diverged phage tail assembly chaperones.
Authors: Pell, L.G. / Cumby, N. / Clark, T.E. / Tuite, A. / Battaile, K.P. / Edwards, A.M. / Chirgadze, N.Y. / Davidson, A.R. / Maxwell, K.L.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Jul 24, 2013Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail assembly chaperone
B: Tail assembly chaperone


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water95553
1
A: Tail assembly chaperone
B: Tail assembly chaperone

A: Tail assembly chaperone
B: Tail assembly chaperone

A: Tail assembly chaperone
B: Tail assembly chaperone

A: Tail assembly chaperone
B: Tail assembly chaperone


Theoretical massNumber of molelcules
Total (without water)117,8988
Polymers117,8988
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.140, 101.140, 63.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Tail assembly chaperone


Mass: 14737.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK97 (virus) / Genus: Lambda-like viruses / Gene: HK97p121 / Plasmid: p11 (modified pET vector) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9MCS6, UniProt: Q9MCS5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2M NH4(OAc), 0.1M Na HEPES pH 7.6, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.979346
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 12, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979346 Å / Relative weight: 1
ReflectionResolution: 2.3→36.8 Å / Num. obs: 13384 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2549 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→36.8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.19 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.288 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29138 710 5 %RANDOM
Rwork0.23198 ---
obs0.23484 13384 98.48 %-
all-27546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.004 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å20 Å2
2---2.44 Å20 Å2
3---4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 0 53 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221744
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9522366
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.78824.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12315320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0161512
X-RAY DIFFRACTIONr_chiral_restr0.1450.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021298
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.2781
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21186
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9761.51101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43421724
X-RAY DIFFRACTIONr_scbond_it2.0683749
X-RAY DIFFRACTIONr_scangle_it3.0174.5639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 49 -
Rwork0.302 899 -
obs--91.68 %
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)
18.6179-2.7498-0.84093.13940.63280.3760.08270.2991-0.241-0.063-0.13440.1660.1094-0.07810.0516-0.11410.01120.0334-0.1430.0572-0.15257.890933.519321.0138
27.88494.75981.80965.24171.18060.4186-0.18230.14930.0365-0.44170.15030.23540.0699-0.11060.032-0.05180.01780.026-0.07710.0335-0.1086-20.706930.112120.3065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1154 - 117
2X-RAY DIFFRACTION2BB1 - 1183 - 120

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