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- PDB-2vld: crystal structure of a repair endonuclease from Pyrococcus abyssi -

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Basic information

Entry
Database: PDB / ID: 2vld
Titlecrystal structure of a repair endonuclease from Pyrococcus abyssi
ComponentsEndonuclease NucS
KeywordsHYDROLASE / ENDONUCLEASE
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
Protein Yojf; Chain: A; - #20 / Protein Yojf; Chain: A; / Endonuclease NucS / : / : / : / Endonuclease NucS C-terminal domain / Endonuclease NucS N-terminal PH-like domain / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 ...Protein Yojf; Chain: A; - #20 / Protein Yojf; Chain: A; / Endonuclease NucS / : / : / : / Endonuclease NucS C-terminal domain / Endonuclease NucS N-terminal PH-like domain / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Distorted Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsRen, B. / Kuhn, J. / Meslet-Cladiere, L. / Briffotaux, J. / Norais, C. / Lavigne, R. / Flament, D. / Ladenstein, R. / Myllykallio, H.
CitationJournal: EMBO J. / Year: 2009
Title: Structure and function of a novel endonuclease acting on branched DNA substrates.
Authors: Ren, B. / Kuhn, J. / Meslet-Cladiere, L. / Briffotaux, J. / Norais, C. / Lavigne, R. / Flament, D. / Ladenstein, R. / Myllykallio, H.
History
DepositionJan 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 26, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_ec / _entity.src_method / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease NucS
B: Endonuclease NucS


Theoretical massNumber of molelcules
Total (without water)58,3042
Polymers58,3042
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-11.5 kcal/mol
Surface area27720 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.966, 100.688, 157.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLUAA3 - 1193 - 119
21LYSLYSGLUGLUBB3 - 1193 - 119
12SERSERPROPROAA126 - 232126 - 232
22SERSERPROPROBB126 - 232126 - 232

NCS ensembles :
ID
1
2

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Components

#1: Protein Endonuclease NucS / Nuclease for ssDNA / UPF0286 PROTEIN PYRAB01260


Mass: 29151.902 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: nucS, PYRAB01260, PAB2263 / Cell line (production host): CodonPlus-RIL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL
References: UniProt: Q9V2E8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 89 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 188 TO MSE ...ENGINEERED RESIDUE IN CHAIN A, ILE 89 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 188 TO MSE ENGINEERED RESIDUE IN CHAIN B, ILE 89 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU 188 TO MSE
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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9077
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 22, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9077 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 19639 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.941 / SU B: 28.058 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.713 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 996 5.2 %RANDOM
Rwork0.243 ---
obs0.243 18306 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.65 Å2
Baniso -1Baniso -2Baniso -3
1-8.38 Å20 Å20 Å2
2---5.97 Å20 Å2
3----2.41 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 0 112 3791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9945026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8965450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81524.078179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30215744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3691533
X-RAY DIFFRACTIONr_chiral_restr0.0990.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022783
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.21605
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22440
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3990.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.21.52334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96323672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.43131556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8894.51354
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A956tight positional0.030.05
12B956tight positional0.030.05
21A858tight positional0.030.05
22B858tight positional0.030.05
11A956tight thermal0.190.5
12B956tight thermal0.190.5
21A858tight thermal0.190.5
22B858tight thermal0.190.5
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 58 -
Rwork0.389 1280 -
obs--99.18 %
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)
12.0253-0.2994-0.02135.1671-0.25642.78110.0012-0.0334-0.24-0.7612-0.2029-0.14020.44090.20180.2016-0.0740.07910.0589-0.01-0.0353-0.034525.626739.509954.6405
20.06240.39330.30033.58320.55183.06540.2742-0.16040.1269-0.7569-0.18790.241-0.34840.4675-0.08630.1457-0.00090.00670.08690.02590.09717.933683.927862.9257
32.03860.06730.56695.30140.28781.9869-0.03110.0650.1814-0.6556-0.14290.6034-0.4786-0.13730.174-0.01570.0893-0.15340.01-0.03530.060115.483657.207554.1444
40.40691.2153-0.9555.9329-1.66662.8531-0.0181-0.0133-0.2153-0.567-0.0646-0.60860.1966-0.090.0827-0.05320.04190.00730.0252-0.04450.177323.246414.11366.5065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 119
2X-RAY DIFFRACTION2A126 - 232
3X-RAY DIFFRACTION3B3 - 119
4X-RAY DIFFRACTION4B126 - 232

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