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- PDB-5oxz: Crystal Structure of NeqN/NeqC complex from Nanoarcheaum equitans... -

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Basic information

Entry
Database: PDB / ID: 5oxz
TitleCrystal Structure of NeqN/NeqC complex from Nanoarcheaum equitans at 1.2A
Components
  • NEQ068
  • NEQ528
KeywordsSPLICING / Intein complex 1
Function / homology
Function and homology information


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 polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B ...Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional 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 / AB INITIO PHASING / Resolution: 1.2 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

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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)16,1182
Polymers16,1182
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-22 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.670, 45.670, 254.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-171-

HOH

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Components

#1: Protein NEQ068


Mass: 12299.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea)
Gene: NEQ068 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74N74
#2: Protein/peptide NEQ528


Mass: 3818.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea)
Gene: NEQ528 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74M37
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.1 M Di-Ammonium Tartrate pH7

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.2→42.41 Å / Num. obs: 51160 / % possible obs: 99.9 % / Redundancy: 12.2 % / Net I/σ(I): 16.2
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.2→42.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.901 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15628 2482 4.9 %RANDOM
Rwork0.13731 ---
obs0.13823 48536 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.092 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.2→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 0 151 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191209
X-RAY DIFFRACTIONr_bond_other_d0.0030.021115
X-RAY DIFFRACTIONr_angle_refined_deg2.6721.9561655
X-RAY DIFFRACTIONr_angle_other_deg1.25332615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0425158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00124.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84115227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.292154
X-RAY DIFFRACTIONr_chiral_restr0.2010.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021406
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02254
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_it2.1890.818580
X-RAY DIFFRACTIONr_mcbond_other2.010.814579
X-RAY DIFFRACTIONr_mcangle_it2.4251.234747
X-RAY DIFFRACTIONr_mcangle_other2.4521.239748
X-RAY DIFFRACTIONr_scbond_it3.7281.183629
X-RAY DIFFRACTIONr_scbond_other3.6821.182629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4211.663905
X-RAY DIFFRACTIONr_long_range_B_refined4.88911.81280
X-RAY DIFFRACTIONr_long_range_B_other4.50811.1371258
X-RAY DIFFRACTIONr_rigid_bond_restr5.92232324
X-RAY DIFFRACTIONr_sphericity_free38.951599
X-RAY DIFFRACTIONr_sphericity_bonded9.75152335
LS refinement shellResolution: 1.198→1.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 188 -
Rwork0.201 3458 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.85910.57850.23531.1145-0.13271.1439-0.02840.037-0.0452-0.07620.0322-0.0520.02930.0135-0.00380.01210.00510.00160.0106-0.00410.00351.617826.7474-5.89
21.10110.9995-0.17541.65830.30260.7287-0.060.0505-0.0568-0.14540.0615-0.1087-0.00770.0632-0.00150.03340.00260.01420.0271-0.00060.0094.371428.7076-12.02
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 83
2X-RAY DIFFRACTION2B2 - 33

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