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- PDB-2j8i: Structure of NP275, a pentapeptide repeat protein from Nostoc pun... -

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Basic information

Entry
Database: PDB / ID: 2j8i
TitleStructure of NP275, a pentapeptide repeat protein from Nostoc punctiforme
ComponentsNP275
KeywordsTOXIN
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: 2.1 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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

Downloads & links

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Assembly

Deposited unit
A: NP275
B: NP275
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0293
Polymers24,9942
Non-polymers351
Water1,874104
1
A: NP275


Theoretical massNumber of molelcules
Total (without water)12,4971
Polymers12,4971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NP275
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5322
Polymers12,4971
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.181, 62.558, 100.549
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


Mass: 12496.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOSTOC PUNCTIFORME (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN SEQUENCE WITH ADDITIONAL 20 RESIDUES AT THE N- TERMINUS TO FACILITATE PURIFICATION.

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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: 33.85 % / Description: NONE
Crystal growpH: 6.8
Details: 30% PEG3350 100 MM NACACODYLATE PH 6.8 200MM LICL2 PROTEIN 25MG/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: 2.1→26.5 Å / Num. obs: 11358 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 8.1 / % possible all: 100

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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 2BM5

2bm5


Resolution: 2.1→100.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.378 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 544 4.8 %RANDOM
Rwork0.188 ---
obs0.191 10813 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2--0.98 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→100.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 1 104 1749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211658
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9712242
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90625.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44515280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.21512
X-RAY DIFFRACTIONr_chiral_restr0.1050.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021262
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21107
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5211.51117
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89821712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6823575
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6054.5530
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 41
Rwork0.207 761
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)
11.5973-0.1315-0.21414.2232.81976.02940.08710.1296-0.0726-0.3676-0.1121-0.0558-0.4598-0.23510.0250.00860.01990.0046-0.23720.013-0.188512.06419.10138.21
21.43-0.99160.45984.4825-2.01363.46210.2181-0.0041-0.0206-0.1071-0.269-0.11650.2863-0.00130.05090.073-0.0155-0.0127-0.246-0.011-0.19568.83123.1829.087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 98
2X-RAY DIFFRACTION2B-12 - 98

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