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- PDB-3ta7: Zinc bound structure of an archaeal member of the LigD 3'-phospho... -

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Basic information

Entry
Database: PDB / ID: 3ta7
TitleZinc bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family
ComponentsATP-dependent DNA ligase, N-terminal domain protein
KeywordsHYDROLASE / 3'-phosphoesterase
Function / homologyDNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / ligase activity / metal ion binding / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / ATP-dependent DNA ligase, N-terminal domain protein
Function and homology information
Biological speciesCandidatus Korarchaeum cryptofilum OPF8 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsDas, U. / Smith, P. / Shuman, S.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Authors: Das, U. / Smith, P. / Shuman, S.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Feb 28, 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 / 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

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Assembly

Deposited unit
A: ATP-dependent DNA ligase, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1174
Polymers13,8501
Non-polymers2673
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.740, 58.570, 32.980
Angle α, β, γ (deg.)90.00, 102.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent DNA ligase, N-terminal domain protein


Mass: 13850.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Korarchaeum cryptofilum OPF8 (archaea)
Gene: Kcr_0736 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1L4V6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystallization was carried out in hanging-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 10 mM ZnCl2 and reservoir solution containing 20% PEG ...Details: Crystallization was carried out in hanging-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 10 mM ZnCl2 and reservoir solution containing 20% PEG 3350 and 0.2 M Na2HPO4 , pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.282 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2011
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.48→32.21 Å / Num. all: 17231 / Num. obs: 16869 / % possible obs: 97.9 % / Observed criterion σ(F): -99 / Observed criterion σ(I): -99 / Redundancy: 2.8 % / Rsym value: 0.028 / Net I/σ(I): 16.8
Reflection shellHighest resolution: 1.48 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 16.8 / Rsym value: 0.028 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_833)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→29.285 Å / SU ML: 0.28 / σ(F): 1.38 / Phase error: 17.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 1737 10.31 %RANDOM
Rwork0.1471 ---
obs0.1503 16852 97.78 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.982 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7302 Å2-0 Å22.4112 Å2
2---2.0522 Å2-0 Å2
3---1.322 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 13 207 1187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131101
X-RAY DIFFRACTIONf_angle_d1.4911491
X-RAY DIFFRACTIONf_dihedral_angle_d13.855446
X-RAY DIFFRACTIONf_chiral_restr0.095151
X-RAY DIFFRACTIONf_plane_restr0.007191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.52360.21791310.16661066X-RAY DIFFRACTION84
1.5236-1.57280.22861450.15811241X-RAY DIFFRACTION97
1.5728-1.6290.18461560.15191261X-RAY DIFFRACTION99
1.629-1.69420.1911630.15561248X-RAY DIFFRACTION99
1.6942-1.77130.19371390.16161268X-RAY DIFFRACTION99
1.7713-1.86460.19911360.16331282X-RAY DIFFRACTION99
1.8646-1.98140.18381530.1481289X-RAY DIFFRACTION99
1.9814-2.13440.18591400.151291X-RAY DIFFRACTION100
2.1344-2.34910.20971430.14821286X-RAY DIFFRACTION100
2.3491-2.68880.19531430.15381282X-RAY DIFFRACTION100
2.6888-3.38680.15951440.13521289X-RAY DIFFRACTION99
3.3868-29.29070.14031440.13661312X-RAY DIFFRACTION99

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