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- PDB-5oxx: Crystal structure of NeqN/NeqC complex from Nanoarcheaum equitans... -

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Basic information

Entry
Database: PDB / ID: 5oxx
TitleCrystal structure of NeqN/NeqC complex from Nanoarcheaum equitans at 1.7A
Components
  • NEQ068
  • NEQ528
KeywordsSPLICING / Intein complex
Function / homology
Function and homology information


DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family ...Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA-directed DNA polymerase / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesNanoarchaeum equitans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsAparicio, D. / Perez-Luque, R. / Ribo, M. / Fita, I.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural Insights into Subunits Assembly and the Oxyester Splicing Mechanism of Neq pol Split Intein.
Authors: Gordo, V. / Aparicio, D. / Perez-Luque, R. / Benito, A. / Vilanova, M. / Uson, I. / Fita, I. / Ribo, M.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEQ068
B: NEQ528


Theoretical massNumber of molelcules
Total (without water)16,1412
Polymers16,1412
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-20 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.434, 67.434, 50.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein NEQ068


Mass: 12316.899 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea)
Strain: Kin4-M / Gene: NEQ068 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74N74
#2: Protein/peptide NEQ528


Mass: 3824.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea)
Strain: Kin4-M / Gene: NEQ528 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74M37
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.79 Å3/Da / Density % sol: 31.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3350 0,2M Ammonium Nitrate pH6.3

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.74→67.43 Å / Num. all: 158183 / Num. obs: 12621 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 22.8
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1803 / CC1/2: 0.904 / Rpim(I) all: 0.39 / Rrim(I) all: 1.027 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OXW

5oxw


Resolution: 1.74→50.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.757 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21884 602 4.8 %RANDOM
Rwork0.20676 ---
obs0.20735 12000 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.318 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2---1.52 Å20 Å2
3---3.04 Å2
Refinement stepCycle: 1 / Resolution: 1.74→50.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 0 37 919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019911
X-RAY DIFFRACTIONr_bond_other_d0.0060.02844
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9661231
X-RAY DIFFRACTIONr_angle_other_deg0.86231966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.4362544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88615165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.344152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02186
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5822.871434
X-RAY DIFFRACTIONr_mcbond_other1.5792.866433
X-RAY DIFFRACTIONr_mcangle_it2.6494.275540
X-RAY DIFFRACTIONr_mcangle_other2.6474.28541
X-RAY DIFFRACTIONr_scbond_it1.693.163477
X-RAY DIFFRACTIONr_scbond_other1.6833.155475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8794.629689
X-RAY DIFFRACTIONr_long_range_B_refined4.73831.159949
X-RAY DIFFRACTIONr_long_range_B_other4.69131.133948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.738→1.783 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 40 -
Rwork0.303 870 -
obs--100 %
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)
10.63170.14810.53291.68710.69160.7973-0.0302-0.03060.1385-0.0464-0.08140.0274-0.01020.02570.11150.07310.0071-0.03260.0501-0.00570.04082.1798-15.141212.7186
21.1564-0.46430.56521.21830.38610.77740.08060.0459-0.0044-0.2768-0.110.0645-0.10530.07330.02940.13080.0082-0.03460.0921-0.0040.00963.5254-18.13314.746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 77
2X-RAY DIFFRACTION2B2 - 30

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