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- PDB-5c10: Nuclease domain of the large terminase subunit gp2 of bacterial v... -

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Basic information

Entry
Database: PDB / ID: 5c10
TitleNuclease domain of the large terminase subunit gp2 of bacterial virus Sf6
ComponentsGene 2 protein
KeywordsMETAL BINDING PROTEIN / nuclease domain / metal binding site / RNAse H
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 nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage Sf6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsZhao, H. / Tang, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM090010 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism.
Authors: Zhao, H. / Lin, Z. / Lynn, A.Y. / Varnado, B. / Beutler, J.A. / Murelli, R.P. / Le Grice, S.F. / Tang, L.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Sep 6, 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 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gene 2 protein


Theoretical massNumber of molelcules
Total (without water)30,7801
Polymers30,7801
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.683, 57.734, 46.654
Angle α, β, γ (deg.)90.000, 98.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gene 2 protein /


Mass: 30779.680 Da / Num. of mol.: 1 / Fragment: nuclease domain (UNP residues 213-470)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Sf6 (virus) / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q716H3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 3.11 Å3/Da / Density % sol: 60.44 % / Description: long rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES, pH7.5, 50mM NaCl, 8% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.55→29.69 Å / Num. obs: 50109 / % possible obs: 97.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.025 / Net I/σ(I): 17.7 / Num. measured all: 184520
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.55-1.573.50.6081.9804522880.8410.3790.8
8.47-29.693.20.03348.79963120.9940.02491.9

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
PHENIX(phenix.refine: 1.8.1_1168)phasing
RefinementResolution: 1.55→19.044 Å / FOM work R set: 0.9006 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1647 2504 5 %Random selection
Rwork0.1445 47562 --
obs0.1455 50066 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.97 Å2 / Biso mean: 30.6 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: final / Resolution: 1.55→19.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 290 2079
Biso mean---44.29 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091856
X-RAY DIFFRACTIONf_angle_d1.1792506
X-RAY DIFFRACTIONf_chiral_restr0.07266
X-RAY DIFFRACTIONf_plane_restr0.006326
X-RAY DIFFRACTIONf_dihedral_angle_d11.211697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57720.24981290.24422473260292
1.5772-1.60930.24241390.21792615275497
1.6093-1.64430.2171360.1992594273097
1.6443-1.68250.1951390.18452635277498
1.6825-1.72460.22511380.1772641277998
1.7246-1.77120.22451380.17862609274798
1.7712-1.82330.18471380.16212633277198
1.8233-1.88210.2171390.15172632277198
1.8821-1.94930.18831400.14892665280598
1.9493-2.02720.18151400.13732659279998
2.0272-2.11940.16011410.13162672281399
2.1194-2.23090.15421400.12622655279599
2.2309-2.37050.1631400.12582659279999
2.3705-2.55310.14521410.13022684282599
2.5531-2.80930.15661410.13572672281398
2.8093-3.21410.1551410.14772678281998
3.2141-4.04310.15591400.12962664280497
4.0431-19.0450.14591440.1492722286698
Refinement TLS params.Method: refined / Origin x: 42.0679 Å / Origin y: 39.8063 Å / Origin z: 24.4122 Å
111213212223313233
T0.1261 Å2-0.0135 Å2-0.0005 Å2-0.1098 Å2-0.0131 Å2--0.1309 Å2
L2.0416 °2-0.3018 °2-0.2463 °2-1.0478 °2-0.0811 °2--2.1531 °2
S0.0026 Å °-0.0345 Å °0.1635 Å °-0.0183 Å °-0.0197 Å °-0.0332 Å °-0.0392 Å °0.0965 Å °0.0234 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 213:454 )

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