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- PDB-5oeb: Structure of large terminase from the thermophilic bacteriophage ... -

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Basic information

Entry
Database: PDB / ID: 5oeb
TitleStructure of large terminase from the thermophilic bacteriophage D6E in complex with ADP (Crystal form 3)
ComponentsLarge subunit terminase
KeywordsVIRAL PROTEIN / large terminase
Function / homologyBacteriophage terminase, large subunit / Terminase large subunit, T4likevirus-type, N-terminal / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / ADENOSINE-5'-DIPHOSPHATE / Large subunit terminase
Function and homology information
Biological speciesDeep-sea thermophilic phage D6E (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsXu, R.G. / Jenkins, H.T. / Greive, S.J. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis.
Authors: Xu, R.G. / Jenkins, H.T. / Antson, A.A. / Greive, S.J.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large subunit terminase
B: Large subunit terminase
C: Large subunit terminase
D: Large subunit terminase
E: Large subunit terminase
F: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,5848
Polymers294,1336
Non-polymers4522
Water1,820101
1
A: Large subunit terminase


Theoretical massNumber of molelcules
Total (without water)49,0221
Polymers49,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4743
Polymers49,0221
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Large subunit terminase


Theoretical massNumber of molelcules
Total (without water)49,0221
Polymers49,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Large subunit terminase


Theoretical massNumber of molelcules
Total (without water)49,0221
Polymers49,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Large subunit terminase


Theoretical massNumber of molelcules
Total (without water)49,0221
Polymers49,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Large subunit terminase


Theoretical massNumber of molelcules
Total (without water)49,0221
Polymers49,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.878, 102.859, 103.029
Angle α, β, γ (deg.)91.130, 117.160, 119.170
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA13 - 41716 - 420
21PROPROBB13 - 41716 - 420
12PHEPHEAA14 - 41717 - 420
22PHEPHECC14 - 41717 - 420
13PROPROAA13 - 41716 - 420
23PROPRODD13 - 41716 - 420
14PROPROAA13 - 41716 - 420
24PROPROEE13 - 41716 - 420
15PROPROAA13 - 41716 - 420
25PROPROFF13 - 41716 - 420
16PHEPHEBB14 - 41717 - 420
26PHEPHECC14 - 41717 - 420
17PROPROBB13 - 41716 - 420
27PROPRODD13 - 41716 - 420
18PROPROBB13 - 41716 - 420
28PROPROEE13 - 41716 - 420
19PROPROBB13 - 41716 - 420
29PROPROFF13 - 41716 - 420
110PHEPHECC14 - 41717 - 420
210PHEPHEDD14 - 41717 - 420
111PHEPHECC14 - 41717 - 420
211PHEPHEEE14 - 41717 - 420
112PHEPHECC14 - 41717 - 420
212PHEPHEFF14 - 41717 - 420
113PROPRODD13 - 41716 - 420
213PROPROEE13 - 41716 - 420
114PROPRODD13 - 41716 - 420
214PROPROFF13 - 41716 - 420
115PROPROEE13 - 41716 - 420
215PROPROFF13 - 41716 - 420

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Large subunit terminase


Mass: 49022.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deep-sea thermophilic phage D6E (virus)
Production host: Escherichia coli (E. coli) / References: UniProt: E5DV50
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.2 M Ammonium Sulfate, 0.1 M HEPES pH 8.0 / PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→45.8 Å / Num. obs: 53693 / % possible obs: 96.4 % / Redundancy: 1.8 % / CC1/2: 0.972 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.164 / Rrim(I) all: 0.232 / Net I/σ(I): 4 / Num. measured all: 95733 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.191.70.832743942930.3360.8321.177194
13.14-45.81.80.0311716460.9960.030.0431588.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.8 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.836 / SU B: 34.679 / SU ML: 0.547 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 2705 5 %RANDOM
Rwork0.2373 ---
obs0.2393 50925 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.42 Å2 / Biso mean: 73.136 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å2-1.44 Å20.73 Å2
2---4.02 Å20.6 Å2
3---4.19 Å2
Refinement stepCycle: final / Resolution: 3.1→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19404 0 28 101 19533
Biso mean--95.63 39.87 -
Num. residues----2424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01919947
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217892
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.93926993
X-RAY DIFFRACTIONr_angle_other_deg0.8862.99941374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36352416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33924.133946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.204153328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3481585
X-RAY DIFFRACTIONr_chiral_restr0.070.22849
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024373
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A273540.05
12B273540.05
21A264880.06
22C264880.06
31A270320.05
32D270320.05
41A264100.06
42E264100.06
51A262180.07
52F262180.07
61B266720.04
62C266720.04
71B271540.05
72D271540.05
81B267000.05
82E267000.05
91B264460.06
92F264460.06
101C264140.05
102D264140.05
111C259920.05
112E259920.05
121C263720.05
122F263720.05
131D265820.04
132E265820.04
141D261780.06
142F261780.06
151E259400.06
152F259400.06
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 149 -
Rwork0.372 3800 -
all-3949 -
obs--97.03 %

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