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- PDB-2vug: The structure of an archaeal homodimeric RNA ligase -

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Basic information

Entry
Database: PDB / ID: 2vug
TitleThe structure of an archaeal homodimeric RNA ligase
ComponentsPAB1020
KeywordsLIGASE / RNA / AMPPNP / PAB1020 / PYROCOCCUS ABYSSI / NUCLEOTIDYL- TRANSFERASE
Function / homology
Function and homology information


Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2250 / Alpha-Beta Plaits - #3360 / Nuclear Transport Factor 2; Chain: A, - #740 / RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / RNA ligase domain, REL/Rln2 / RNA ligase / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2250 / Alpha-Beta Plaits - #3360 / Nuclear Transport Factor 2; Chain: A, - #740 / RNA ligase, Pab1020 family / RNA ligase Pab1020, C-terminal domain / Ligase Pab1020 C-terminal region / RNA ligase domain, REL/Rln2 / RNA ligase / Dna Ligase; domain 1 - #70 / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nuclear Transport Factor 2; Chain: A, / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Plaits / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP-dependent DNA ligase
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsBrooks, M.A. / Meslet-Cladiere, L. / Graille, M. / Kuhn, J. / Blondeau, K. / Myllykallio, H. / van Tilbeurgh, H.
CitationJournal: Protein Sci. / Year: 2008
Title: The structure of an archaeal homodimeric ligase which has RNA circularization activity.
Authors: Brooks, M.A. / Meslet-Cladiere, L. / Graille, M. / Kuhn, J. / Blondeau, K. / Myllykallio, H. / van Tilbeurgh, H.
History
DepositionMay 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_id_ISSN ..._audit_author.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
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 / _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

Downloads & links

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Assembly

Deposited unit
A: PAB1020
B: PAB1020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,69611
Polymers90,8572
Non-polymers1,8409
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-46.8 kcal/mol
Surface area41590 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.962, 103.257, 150.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A7 - 382
2111B7 - 382

NCS oper: (Code: given
Matrix: (-0.98653, -0.00159, -0.16356), (0.00037, -0.99997, 0.00749), (-0.16356, 0.00733, 0.98651)
Vector: 64.7938, 77.48051, 5.04134)

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Components

#1: Protein PAB1020


Mass: 45428.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: EACH MONOMER OF PAB1020 IS BOUND TO ONE MOLECULE OF PHOSPHOAMINO PHOSPHONIC ACID-ADENYLATE ESTER (AMPPNP)
Source: (gene. exp.) PYROCOCCUS ABYSSI GE5 (archaea) / Plasmid: PQE-80L / Cell line (production host): SURE RIL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UYG2
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 52.99 % / Description: NONE
Crystal growpH: 8
Details: 50% METHANE PENTANE-DIOL (MPD), 0-0.2M NH4H2PO4 AND 0.1M TRIS-CL, PH 8.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 20985 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.883 / SU B: 18.058 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES IN CHAINS A, B: 10, 36, 37, 38.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1082 5.2 %RANDOM
Rwork0.224 ---
obs0.227 19844 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2---0.73 Å20 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 118 10 6222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2732.0048538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2135744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91123.4300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.567151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0181554
X-RAY DIFFRACTIONr_chiral_restr0.0830.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024690
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.23111
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.24356
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3981.53782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42426019
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.64532827
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4564.52519
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3039 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.30.5
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 76
Rwork0.311 1398

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