Mass: 10007.484 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-86 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BE23 / References: UniProt: Q02078
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Type: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPTS. (4) 2D 12C-FILTERED ...Type: (1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPTS. (4) 2D 12C-FILTERED EXPERIMENTS FOR DNA ASSIGNMENTS. (5) IPAP EXPTS FOR DIPOLAR COUPLINGS DIPOLAR COUPLINGS WERE MEASURED IN A BICELLE LIQUID CRYSTALLINE MEDIUM.
NMR details
Text: SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 4560 EXPERIMENTAL NMR RESTRAINTS (I.E. 2280 UNIQUE ONES SINCE PROTEIN IS A HOMODIMER AND DNA IS PALINDROMIC). NOE RESTRAINTS: (A) PROTEIN: 664 ...Text: SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 4560 EXPERIMENTAL NMR RESTRAINTS (I.E. 2280 UNIQUE ONES SINCE PROTEIN IS A HOMODIMER AND DNA IS PALINDROMIC). NOE RESTRAINTS: (A) PROTEIN: 664 SEQUENTIAL, 504 MEDIUM RANGE, 212 LONG RANGE, 616 INTRARESIDUE, 174 INTERSUBUNIT. (B) DNA: 428 INTRARESIDUE, 196 SEQUENTIAL INTRASTRAND, 24 INTERSTRAND. (C) PROTEIN- DNA 168. H-BOND RESTRAINTS: PROTEIN 138, DNA 120. TORSION ANGLE RESTRAINTS: PROTEIN 480 (142 PHI, 142 PSI, 112 CHI1, 68 CHI2, 16 CHI3), DNA 228. THREE-BOND HN-HALPHA COUPLING CONSTANTS: 72. SECONDARY 13C SHIFTS: 140 13CALPHA, 140 13CBETA. DIPOLAR COUPLINGS: 1DNH PROTEIN: 70, 1DCH DNA 70. REPULSIVE RESTRAINTS: 106
Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM XPLOR/CNS MODIFIED TO INCORPORATE COUPLING CONSTANT ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM XPLOR/CNS MODIFIED TO INCORPORATE COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT RESTRAINTS, (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J. MAGN. RESON 131, 159-162 (1998); J. MAGN 133, 216-221 (1998)), AND A CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. PROTEIN SCI. 5, 1067-1080 (1996); J. MAGN. RESON 125, 171-177 (1997)). IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. THE LATTER ARE OBTAINED BY TAKING THE AVERAGE OF THE 35 SIMULATED ANNEALING STRUCTURES BEST-FITTED TO RESIDUES 1-73 AND 101-173 OF THE PROTEIN AND RESIDUES 201-240 OF THE DNA. RESIDUES 74-85 AND 174-185 ARE DISORDERED IN SOLUTION AND ARE THEREFORE NOT INCLUDED IN THE COORDINATES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAINED BY RESTRAINED REGULARIZATION OF THE AVERAGE COORDINATES AGAINST THE SAME TARGET FUNCTION USED TO CALCULATE THE SIMULATED ANNEALING STRUCTURES.
NMR ensemble
Conformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 35 / Conformers submitted total number: 1
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi