#PDBScan Report for: /share/apps/genapp/sassie2/results/users/dww100/no_project_specified/1008.pdb ##Structure Preparedness for Simulation ------------------------------------------------------------------------------- Chain Moltype Missing Residues Non-CHARMM Residues Missing Heavy Atoms ----- ---------- -------------------- ------------------- --------------------- A Protein 3 1 0 ----- ---------- -------------------- ------------------- --------------------- Oh No! There are critical issues with this PDB! This PDB is **NOT** ready for simulation. 1. Some protein hydrogens are missing - please consult NO_HEADER_PDBSCAN report 2. Non CHARMM standard residues detected 3. Missing residues - see table above and full report for details ### Warnings 1. BIOMT present - PDB may not represent the biological unit, see report below 2. Chains missing segment names will have these created from the chain ID ##Summary *CRYSTAL STRUCTURE OF PROJECT ID PH1539 FROM PYROCOCCUS HORIKOSHII OT3* -------------------------------------------------------------------------------- Header HYDROLASE -------------------- ----------------------------------------------------------- Citation K.SHIMIZU,C.KUROISHI,M.SUGAHARA,N.KUNISHIMA "STRUCTURE OF PEPTIDYL-TRNA HYDROLASE 2 FROM PYROCOCCUS HORIKOSHII OT3: INSIGHT INTO THE FUNCTIONAL ROLE OF ITS DIMERIC STATE." ACTA CRYSTALLOGR.,SECT.D V. 64 444 2008 [Link](http://dx.doi.org/10.1107/S0907444908002850) Method X-Ray Diffraction Experiment Resolution 1.20 Angstrom; R-factor 19.30; Free R-factor 21.50; Space Group P 41 21 2 -------------------- ----------------------------------------------------------- ##Polymers -------------------------------------------------------------------------------- Chain ID Name Type No. % Residues Sequence Observed Residues ---------- ------------------------------------ ---------- ---------- ---------- A PEPTIDYL-TRNA HYDROLASE Protein 121 98 ---------- ------------------------------------ ---------- ---------- ---------- ##Heterogens Heterogens may not be included as standard in forcefields. -------------------------------------------------------------------------------- Residue Name Chain IDs ---------- ---------------------------------------------------------- ---------- NA SODIUM ION A ---------- ---------------------------------------------------------- ---------- ##System statistics Metrics derived from PDB coordinates: -------------------------------------------------------------------------------- Measurement Value ------------------- ------------------------------------------------------------ Number of models 1 Mass 15324.48 Centre of mass 17.85 16.43 33.52 Radius of gyration 14.96 Coordinate minimums 0.88 -6.20 14.78 Coordinate maximums 38.28 40.67 49.46 ------------------- ------------------------------------------------------------ ___ ##Biological Unit **Biomolecule: 1 - Author asserted biological unit for chain A: Dimeric** -------------------------------------------------------------------------------- # Rotation Translation ----- ----------------------------------------------- -------------------------- 1 1.000000 0.000000 0.000000 0.00000 1 0.000000 1.000000 0.000000 0.00000 1 0.000000 0.000000 1.000000 0.00000 2 0.000000 1.000000 0.000000 0.00000 2 1.000000 0.000000 0.000000 0.00000 2 0.000000 0.000000 -1.000000 85.79100 ----- ----------------------------------------------- -------------------------- ___ ##Chain Information Sequences provided in FASTA format * Residues shown in lower case are missing coordinates * 'X' = unknown residue or HETATM * '-' = no residue (filler for easier reading) ###Chain A *Sequence:* --------------------------------------------------------------- `123456789|123456789|123456789|123456789|123456789|` ---------- ---------------------------------------------------- 1 `mikMFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAW` 51 `FREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTV` 101 `LAVGPAPEEIVDKVTGNLKLL-----------------------------` 151 `--------------------------------------------------` 201 `--------------------------------------------------` 251 `--------------------------------------------------` 301 `--------------------------------------------------` 351 `--------------------------------------------------` 401 `--------------------------------------------------` 451 `--------------------------------------------------` 501 `--------------------------------------------------` 551 `--------------------------------------------------` 601 `--------------------------------------------------` 651 `--------------------------------------------------` 701 `--------------------------------------------------` 751 `--------------------------------------------------` 801 `--------------------------------------------------` 851 `--------------------------------------------------` 901 `--------------------------------------------------` 951 `--------------------------------------------------` 1001 `XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX` 1051 `XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX` 1101 `XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX` 1151 `XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ` ---------- ---------------------------------------------------- *Gaps:* 1-3 *Heterogens:* -------------------------------------------------------------------------------- Residue No. Resdiue ID Description -------------------- ---------- ------------------------------------------------ 1001 NA SODIUM ION 1002-1188 HOH Water -------------------- ---------- ------------------------------------------------ ##Chain statistics Metrics derived from PDB coordinates: -------------------------------------------------------------------------------- Measurement Value ------------------- ------------------------------------------------------------ Number of models 1 Mass 15324.48 Centre of mass 17.85 16.43 33.52 Radius of gyration 14.96 Coordinate minimums 0.88 -6.20 14.78 Coordinate maximums 38.28 40.67 49.46 ------------------- ------------------------------------------------------------ ___