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- PDB-5c15: K428A mutant nuclease domain of the large terminase subunit gp2 o... -

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Basic information

Entry
Database: PDB / ID: 5c15
TitleK428A mutant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese
ComponentsGene 2 protein
KeywordsMETAL BINDING PROTEIN / nuclease domain / metal binding site
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: 1.57 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 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 15, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct / struct_conn
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.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)30,8003
Polymers30,6911
Non-polymers1102
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.766, 57.365, 46.646
Angle α, β, γ (deg.)90.000, 98.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gene 2 protein /


Mass: 30690.609 Da / Num. of mol.: 1 / Fragment: nuclease domain (UNP residues 213-470) / Mutation: D251A, D348Q, K428A
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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.86 Å3/Da / Density % sol: 57 % / Description: long rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES, pH 7.5, 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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 47321 / % possible obs: 97.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 27
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data collection
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX(phenix.refine: 1.8.1_1168)phasing
RefinementResolution: 1.57→18.922 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2367 5 %Random selection
Rwork0.1636 44954 --
obs0.1647 47321 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.32 Å2 / Biso mean: 36.0886 Å2 / Biso min: 15.84 Å2
Refinement stepCycle: final / Resolution: 1.57→18.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 2 277 2028
Biso mean--46.07 47.76 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091792
X-RAY DIFFRACTIONf_angle_d1.1732411
X-RAY DIFFRACTIONf_chiral_restr0.047256
X-RAY DIFFRACTIONf_plane_restr0.006312
X-RAY DIFFRACTIONf_dihedral_angle_d10.85667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.60210.32281220.31282320244286
1.6021-1.63690.31841350.28092555269095
1.6369-1.67490.2821400.25952660280099
1.6749-1.71680.24581410.24642670281199
1.7168-1.76320.26071390.22462655279499
1.7632-1.8150.22021400.20352653279399
1.815-1.87360.20121410.18832689283099
1.8736-1.94050.21341420.18752685282799
1.9405-2.01810.15651410.172826822823100
2.0181-2.10980.19781430.159527042847100
2.1098-2.22090.15761410.15426942835100
2.2209-2.35980.16381420.151326842826100
2.3598-2.54160.18741410.15372691283299
2.5416-2.79660.18011420.15772686282899
2.7966-3.19960.17531400.16482663280398
3.1996-4.02480.17851390.14282653279297
4.0248-18.92320.17131380.14672610274894
Refinement TLS params.Method: refined / Origin x: 41.8693 Å / Origin y: 39.7796 Å / Origin z: 24.5443 Å
111213212223313233
T0.1442 Å2-0.0118 Å20.0044 Å2-0.1494 Å2-0.0145 Å2--0.1448 Å2
L1.7586 °2-0.2442 °2-0.1348 °2-0.9787 °2-0.1709 °2--1.9562 °2
S-0.0016 Å °-0.0423 Å °0.1211 Å °0.0011 Å °-0.0217 Å °-0.0292 Å °-0.0437 Å °0.0969 Å °0.019 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 213:453 )

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