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- PDB-2kpm: Solution NMR Structure of uncharacterized protein from gene locus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2kpm | ||||||
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Title | Solution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / methods development / uncharacterized protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | ![]() NYN domain, MARF1-type / NYN domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics, molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Rossi, P. / Belote, R. / Jiang, M. / Xiao, R. / Ciccosanti, C. / Acton, T. / Everett, J. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Solution NMR Structure of uncharacterized protein from gene locus NE0665 of Nitrosomonas europaea. Northeast Structural Genomics Target NeR103A Authors: Rossi, P. / Xiao, R. / Acton, T. / Rost, B. / Montelione, G.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 737.7 KB | Display | ![]() |
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PDB format | ![]() | 626.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.8 KB | Display | ![]() |
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Full document | ![]() | 470.2 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 51.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 11939.336 Da / Num. of mol.: 1 / Fragment: sequence database residues 174-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG). CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT. |
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Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics, molecular dynamics / Software ordinal: 1 Details: Iterative noesy assignment followed by torsion angle dynamics in CYANA-3.0, STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES ...Details: Iterative noesy assignment followed by torsion angle dynamics in CYANA-3.0, STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 86.63%, SIDECHAIN 76.84%, AROMATIC (SC) 100%, STEREOSPECIFIC VL METHYL ASSIGNMENT 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2412 NOE, 230 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 8.1 DEG. 3 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 19-98. SECONDARY STRUCTURE - ALPHA HELICES: 23-32, 42-52, 66-72. BETA STRANDS: 40-41, 90-96, 77-83. RMSD(ANG): BACKBONE 0.4, ALL HEAVY ATOMS 0.7. RAMA. DISTRIBUTION (MOLPROBITY): 97/3/0/0 PROCHECK (PSI-PHI): -0.12/-0.16 (RAW/Z), PROCHECK (ALL): 0.04/0.24 (RAW/Z), MOLPROBITY CLASH: 9.92/-0.18 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.91, PRECISION: 0.93, F-MEASURE: 0.92, DP-SCORE: 0.79. | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |