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- PDB-2j8k: Structure of the fusion of NP275 and NP276, pentapeptide repeat p... -

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Basic information

Entry
Database: PDB / ID: 2j8k
TitleStructure of the fusion of NP275 and NP276, pentapeptide repeat proteins from Nostoc punctiforme
ComponentsNP275-NP276
KeywordsTOXIN / NOSTOC PUNCTIFORME / PENTAPEPTIDE REPEAT PROTEIN / PRP / RIGHT HANDED QUADRILATERAL BETA HELIX / RHQBH
Function / homologyE3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Function and homology information
Biological speciesNOSTOC PUNCTIFORME (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVetting, M.W. / Hegde, S.S. / Hazleton, K.Z. / Blanchard, J.S.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural Characterization of the Fusion of Two Pentapeptide Repeat Proteins, Np275 and Np276, from Nostoc Punctiforme: Resurrection of an Ancestral Protein.
Authors: Vetting, M.W. / Hegde, S.S. / Hazleton, K.Z. / Blanchard, J.S.
History
DepositionOct 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NP275-NP276
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3723
Polymers21,0811
Non-polymers2912
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.605, 55.470, 58.989
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 NP275-NP276


Mass: 21081.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM NP275, RESIDUES 107-181 ORIGINATE FROM NP276. INTERVENING RESIDUES ORIGINATE FROM PREVIOUSLY ...Details: MUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM NP275, RESIDUES 107-181 ORIGINATE FROM NP276. INTERVENING RESIDUES ORIGINATE FROM PREVIOUSLY NON-CODING DNA SEQUENCE BETWEEN NP275 AND NP276.
Source: (gene. exp.) NOSTOC PUNCTIFORME (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM ...MUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM NP275, RESIDUES 107-181 ORIGINATE FROM NP276. INTERVENING RESIDUES ORIGINATE FROM PREVIOUSLY NON-CODING DNA SEQUENCE BETWEEN NP275 AND NP276. INCLUDES N-TERMINAL RESIDUES ORIGINATING FROM 20 RESIDUE HEXAHISTIDINE TAG.

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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: 1.87 Å3/Da / Density % sol: 33.66 % / Description: NONE
Crystal growpH: 6.5
Details: 1.6 M AMMONIUM SULFATE 100 MM MES PH 6.5 PROTEIN 10 MG/ML

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Data collection

DiffractionMean temperature: 194 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→15.9 Å / Num. obs: 26666 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 31.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 11.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8I

2j8i


Resolution: 1.5→59.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.976 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.PROTEIN IS A MONOMER IN SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1343 5 %RANDOM
Rwork0.174 ---
obs0.175 25323 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→59.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 17 150 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211415
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9811932
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1375197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56626.76171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79615237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.346158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021085
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.2664
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2977
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.961.5949
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37521470
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9723487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6534.5458
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
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 90
Rwork0.3 1825

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