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- PDB-5c2f: K428A mutant nuclease domain of the large terminase subunit gp2 o... -

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Basic information

Entry
Database: PDB / ID: 5c2f
TitleK428A mutant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese and beta-thujaplicinol
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
Chem-JTH / : / Gene 2 protein
Similarity search - Component
Biological speciesEnterobacteria phage Sf6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 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 15, 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 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_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.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.value / _struct_conn.pdbx_dist_value / _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

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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)31,0124
Polymers30,7221
Non-polymers2903
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.589, 58.418, 53.384
Angle α, β, γ (deg.)90.000, 96.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gene 2 protein /


Mass: 30721.578 Da / Num. of mol.: 1 / Fragment: nuclease domain (UNP residues 213-470) / Mutation: 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: Chemical ChemComp-JTH / 2,7-dihydroxy-4-(propan-2-yl)cyclohepta-2,4,6-trien-1-one / beta-thujaplicinol


Mass: 180.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
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: 1.03361 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03361 Å / Relative weight: 1
ReflectionResolution: 1.86→28.79 Å / Num. obs: 22914 / % possible obs: 95.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Net I/σ(I): 17.1 / Num. measured all: 79416
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
1.86-1.93.10.5882399412900.690.39285.2
8.92-28.793.40.02251.97152110.9980.01491.1

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
Cootmodel building
RefinementResolution: 1.86→19.256 Å / FOM work R set: 0.8654 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1145 5 %Random selection
Rwork0.1682 21751 --
obs0.1702 22896 95.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.3 Å2 / Biso mean: 35.59 Å2 / Biso min: 15.42 Å2
Refinement stepCycle: final / Resolution: 1.86→19.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 15 128 1928
Biso mean--35.2 45.16 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071847
X-RAY DIFFRACTIONf_angle_d1.0632491
X-RAY DIFFRACTIONf_chiral_restr0.078263
X-RAY DIFFRACTIONf_plane_restr0.004323
X-RAY DIFFRACTIONf_dihedral_angle_d13.419687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.94530.29111330.26542535266890
1.9453-2.04780.26051430.21492721286496
2.0478-2.17590.25071440.17472731287597
2.1759-2.34370.20761460.17212772291897
2.3437-2.5790.22361460.16742764291097
2.579-2.95110.2051440.16962750289497
2.9511-3.71370.21951420.16382690283294
3.7137-19.25710.17251470.15152788293596
Refinement TLS params.Method: refined / Origin x: -0.6663 Å / Origin y: 11.8365 Å / Origin z: -12.2168 Å
111213212223313233
T0.1417 Å2-0.0168 Å20.0105 Å2-0.1507 Å20.0249 Å2--0.1361 Å2
L2.8373 °2-0.1376 °20.5697 °2-1.7862 °20.3866 °2--1.9462 °2
S0.0044 Å °0.1818 Å °0.1241 Å °-0.0742 Å °-0.0111 Å °0.0154 Å °-0.153 Å °0.0151 Å °-0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 213:454 OR RESID 601:728 OR RESID 503:503 OR RESID 501:502 ) )A213 - 454
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 213:454 OR RESID 601:728 OR RESID 503:503 OR RESID 501:502 ) )A601 - 728
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 213:454 OR RESID 601:728 OR RESID 503:503 OR RESID 501:502 ) )A503
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 213:454 OR RESID 601:728 OR RESID 503:503 OR RESID 501:502 ) )A501 - 502

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