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- PDB-4iee: Crystal Structure of the large terminase subunit gp2 of bacterial... -

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Basic information

Entry
Database: PDB / ID: 4iee
TitleCrystal Structure of the large terminase subunit gp2 of bacterial virus Sf6 complexed with ATP-r-S
ComponentsGene 2 protein
KeywordsVIRAL PROTEIN / DNA packaging / terminase / ATPase / nuclease / ATP-r-S binding / Magnesium binding
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Terminase RNAseH like domain / Phage terminase large subunit, N-terminal / Phage terminase large subunit / Bacteriophage terminase, large subunit / Nucleotidyltransferase; domain 5 - #240 / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Terminase RNAseH like domain / Phage terminase large subunit, N-terminal / Phage terminase large subunit / Bacteriophage terminase, large subunit / Nucleotidyltransferase; domain 5 - #240 / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Gene 2 protein
Similarity search - Component
Biological speciesShigella phage Sf6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 Å
AuthorsZhao, H. / Christensen, T. / Kamau, Y. / Tang, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage.
Authors: Zhao, H. / Christensen, T.E. / Kamau, Y.N. / Tang, L.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gene 2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7953
Polymers55,2481
Non-polymers5482
Water6,954386
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.101, 63.142, 149.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Gene 2 protein /


Mass: 55247.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf6 (virus) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q716H3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris, 15% ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.89→100 Å / Num. all: 44206 / Num. obs: 43101 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.87 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 29.92
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.29 / Num. unique all: 1987 / % possible all: 91.7

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4IDH

4idh


Resolution: 1.89→19.748 Å / SU ML: 0.22 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.29 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 2088 4.97 %RANDOM
Rwork0.1655 ---
obs0.1676 42048 95.35 %-
all-43101 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.93 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 28.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.5331 Å20 Å2-0 Å2
2--0.3161 Å2-0 Å2
3----1.8492 Å2
Refinement stepCycle: LAST / Resolution: 1.89→19.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 32 386 4022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073747
X-RAY DIFFRACTIONf_angle_d1.0365078
X-RAY DIFFRACTIONf_dihedral_angle_d16.7321441
X-RAY DIFFRACTIONf_chiral_restr0.075547
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93370.26741100.22332275X-RAY DIFFRACTION83
1.9337-1.9820.26921270.18782405X-RAY DIFFRACTION87
1.982-2.03550.23171360.16282535X-RAY DIFFRACTION92
2.0355-2.09540.18491310.15172608X-RAY DIFFRACTION95
2.0954-2.16290.2391390.15852641X-RAY DIFFRACTION96
2.1629-2.24010.21141410.1572678X-RAY DIFFRACTION96
2.2401-2.32970.21081400.15812684X-RAY DIFFRACTION97
2.3297-2.43550.21761420.16232711X-RAY DIFFRACTION98
2.4355-2.56370.21261420.1682730X-RAY DIFFRACTION99
2.5637-2.72390.22611470.16652766X-RAY DIFFRACTION99
2.7239-2.93360.19451440.1682745X-RAY DIFFRACTION99
2.9336-3.22770.18721470.16822780X-RAY DIFFRACTION99
3.2277-3.69210.20841460.16272793X-RAY DIFFRACTION99
3.6921-4.64170.18031480.15142804X-RAY DIFFRACTION98
4.6417-19.74960.21421480.17922805X-RAY DIFFRACTION94
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)
10.95620.18250.13851.2197-0.03811.82810.0585-0.0341-0.08510.0899-0.0116-0.0906-0.01470.1669-0.04620.16520.0234-0.02250.1377-0.00120.13829.090443.286225.4727
20.6029-0.2369-0.16761.1957-0.63270.5573-0.0654-0.33-0.12980.1740.16660.1763-0.0663-0.2063-0.10030.16970.0122-0.00190.19850.06940.14418.636635.346545.8648
30.80730.0118-0.10551.09260.00970.93040.0136-0.02040.005-0.007-0.0078-0.00910.0522-0.0075-0.00550.0208-0.0065-0.01890.0433-0.0150.029346.839.076166.7349
44.33340.24751.58761.00720.18355.7697-0.6497-0.0189-0.05810.2298-0.1264-0.00760.19060.08550.46760.454-0.08360.03240.3348-0.03640.286318.673935.239532.673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 4:173)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 174:211)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 212:466)A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 502:502)A0

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