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- PDB-3tal: Crystal structure of NurA with manganese -

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Basic information

Entry
Database: PDB / ID: 3tal
TitleCrystal structure of NurA with manganese
ComponentsDNA double-strand break repair protein nurA
KeywordsHYDROLASE / Recombination
Function / homology
Function and homology information


exonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / metal ion binding
Similarity search - Function
DNA double-strand break repair nuclease NurA-like / NurA domain / NurA domain / NurA
Similarity search - Domain/homology
: / DNA double-strand break repair nuclease NurA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 Å
AuthorsChae, J. / Kim, Y.C. / Cho, Y.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure of the NurA-dAMP-Mn2+ complex
Authors: Chae, J. / Kim, Y.C. / Cho, Y.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: 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_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: DNA double-strand break repair protein nurA
B: DNA double-strand break repair protein nurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8687
Polymers108,5562
Non-polymers3125
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-58 kcal/mol
Surface area38020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.803, 114.654, 121.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA double-strand break repair protein nurA / Putative uncharacterized protein


Mass: 54278.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1168 / Plasmid: pET-28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1N8
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% PEG 400, 0.1M Tris-HCl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2010
RadiationMonochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 16937 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 97.95 Å2
Reflection shellResolution: 3.1→3.15 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 3.15→29.478 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 1584 10.08 %RANDOM
Rwork0.2181 ---
obs0.225 15717 96.76 %-
all-16214 --
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 98.987 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.7641 Å20 Å20 Å2
2--7.4454 Å20 Å2
3---2.3187 Å2
Refinement stepCycle: LAST / Resolution: 3.15→29.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 0 10 20 6861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066956
X-RAY DIFFRACTIONf_angle_d1.2969373
X-RAY DIFFRACTIONf_dihedral_angle_d17.5662686
X-RAY DIFFRACTIONf_chiral_restr0.0871079
X-RAY DIFFRACTIONf_plane_restr0.0051178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1501-3.25160.4361290.3235115089
3.2516-3.36770.40821350.2629123393
3.3677-3.50230.32271410.2204121295
3.5023-3.66140.30171480.2277128997
3.6614-3.85410.33721470.2263125697
3.8541-4.0950.3041390.2021129698
4.095-4.41020.22761470.1921129898
4.4102-4.85220.2751400.18481313100
4.8522-5.55030.33071420.22133799
5.5503-6.97740.32891540.26821343100
6.9774-29.4790.2221620.2022140698
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)
11.61960.3361-0.3176-0.0151-0.14893.9392-0.13950.1294-0.0420.1491-0.0986-0.12110.0431-0.0522-0.0470.38870.07270.02450.1563-0.02830.313253.12558.277378.4767
21.3595-0.3422-0.32371.26880.77053.29740.0157-0.26340.19430.1455-0.0760.0914-0.5090.3020.01770.4979-0.0955-0.0310.467-0.16330.469759.48871.1037104.091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:439)
2X-RAY DIFFRACTION2chain 'B' and (resseq 5:440)

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