PDB Short entry for 2B7T HEADER HYDROLASE 05-OCT-05 2B7T TITLE STRUCTURE OF ADAR2 DSRBM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC EDITASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOUBLE-STRANDED RNA-BINDING DOMAIN; COMPND 5 SYNONYM: DSRNA ADENOSINE DEAMINASE, RNA EDITING DEAMINASE 1, RNA COMPND 6 EDITING ENZYME 1; COMPND 7 EC: 3.5.-.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: ADARB1, RED1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET16 KEYWDS RNA EDITING, RNA-BINDING PROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.STEFL,M.XU,L.SKRISOVSKA,R.B.EMESON,F.H.-T.ALLAIN REVDAT 3 09-MAR-22 2B7T 1 REMARK REVDAT 2 24-FEB-09 2B7T 1 VERSN REVDAT 1 14-MAR-06 2B7T 0 JRNL AUTH R.STEFL,M.XU,L.SKRISOVSKA,R.B.EMESON,F.H.-T.ALLAIN JRNL TITL STRUCTURE AND SPECIFIC RNA BINDING OF ADAR2 DOUBLE-STRANDED JRNL TITL 2 RNA BINDING MOTIFS. JRNL REF STRUCTURE V. 14 345 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16472753 JRNL DOI 10.1016/J.STR.2005.11.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA, SPARKY, AMBER 7 REMARK 3 AUTHORS : CASE, D.A., ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2B7T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034782. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 8.0 REMARK 210 IONIC STRENGTH : 250MM TOTAL SALT REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM U-15N; 200MM NACL; 50 MM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O; 1MM U-15N,13C; 200MM NACL; REMARK 210 50 MM PHOSPHATE BUFFER, 90% H2O, REMARK 210 10% D2O; 1MM U-15N; 200MM NACL; REMARK 210 50 MM PHOSPHATE BUFFER, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D 15N-SEPARATED REMARK 210 NOESY; 3D 13C-SEPARATED NOESY; REMARK 210 15N-HSQC; 13C-HSQC; HNCA; HNCO; REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 2D REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 5 PRO A 1 CA - N - CD ANGL. DEV. = -8.5 DEGREES REMARK 500 7 PRO A 1 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 7 VAL A 37 CA - CB - CG2 ANGL. DEV. = 9.9 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -10.0 DEGREES REMARK 500 10 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 PRO A 1 CA - N - CD ANGL. DEV. = -8.7 DEGREES REMARK 500 20 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 VAL A 4 6.40 -66.81 REMARK 500 1 PRO A 6 99.23 -33.35 REMARK 500 1 LYS A 7 -73.36 -46.66 REMARK 500 1 GLN A 27 125.79 -32.87 REMARK 500 1 THR A 28 -159.15 -155.79 REMARK 500 1 PRO A 30 23.82 -71.87 REMARK 500 1 VAL A 31 -29.35 69.67 REMARK 500 1 ASN A 43 -3.41 -172.85 REMARK 500 1 PRO A 52 2.72 -64.52 REMARK 500 1 GLN A 71 -33.88 -138.68 REMARK 500 1 PHE A 72 159.32 54.13 REMARK 500 2 PRO A 3 0.62 -65.27 REMARK 500 2 PRO A 18 49.95 -75.91 REMARK 500 2 GLN A 27 125.35 -33.05 REMARK 500 2 THR A 28 17.69 -154.78 REMARK 500 2 ALA A 33 52.94 -154.60 REMARK 500 2 ASN A 43 -14.28 -166.68 REMARK 500 2 PRO A 52 10.66 -54.74 REMARK 500 3 HIS A 32 -3.83 -141.15 REMARK 500 3 ALA A 33 52.92 -153.17 REMARK 500 3 ASN A 43 -10.39 -169.72 REMARK 500 3 PRO A 52 11.80 -67.35 REMARK 500 3 GLN A 71 -25.28 54.59 REMARK 500 4 PRO A 30 35.49 -87.34 REMARK 500 4 VAL A 31 -33.97 65.80 REMARK 500 4 ASN A 43 -13.93 -168.06 REMARK 500 4 PRO A 52 20.50 -69.39 REMARK 500 4 THR A 53 148.03 -173.40 REMARK 500 4 GLN A 71 -8.45 -140.39 REMARK 500 5 PRO A 3 27.98 -60.11 REMARK 500 5 LEU A 5 150.95 59.67 REMARK 500 5 LYS A 7 -87.07 -22.62 REMARK 500 5 SER A 26 104.26 14.44 REMARK 500 5 THR A 28 -149.61 -157.01 REMARK 500 5 PRO A 30 36.64 -78.67 REMARK 500 5 VAL A 31 -6.91 69.56 REMARK 500 5 ASN A 43 -8.09 -172.48 REMARK 500 5 PRO A 52 2.65 -66.77 REMARK 500 6 ALA A 33 49.89 -151.16 REMARK 500 6 ASN A 43 -6.68 -171.88 REMARK 500 6 PRO A 52 12.55 -57.08 REMARK 500 6 THR A 53 19.79 -163.82 REMARK 500 6 LYS A 54 -38.22 52.93 REMARK 500 6 PHE A 72 102.90 18.28 REMARK 500 7 LYS A 7 -35.52 -37.84 REMARK 500 7 VAL A 31 -51.26 62.23 REMARK 500 7 ASN A 43 -15.26 -173.20 REMARK 500 7 PRO A 52 6.24 -65.28 REMARK 500 7 GLN A 71 -22.39 107.06 REMARK 500 8 LEU A 5 -37.64 -157.27 REMARK 500 REMARK 500 THIS ENTRY HAS 126 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 6 LYS A 7 1 -139.97 REMARK 500 LEU A 25 SER A 26 1 -121.56 REMARK 500 LEU A 25 SER A 26 2 -128.68 REMARK 500 LEU A 25 SER A 26 3 -119.25 REMARK 500 LEU A 25 SER A 26 4 -121.24 REMARK 500 GLY A 44 GLN A 45 4 -143.56 REMARK 500 ALA A 33 PRO A 34 5 149.31 REMARK 500 LEU A 25 SER A 26 6 -127.50 REMARK 500 LEU A 25 SER A 26 7 -127.23 REMARK 500 LEU A 25 SER A 26 8 -136.71 REMARK 500 PRO A 6 LYS A 7 9 -145.73 REMARK 500 LEU A 25 SER A 26 9 -119.62 REMARK 500 LEU A 25 SER A 26 11 -129.11 REMARK 500 LEU A 25 SER A 26 12 -123.37 REMARK 500 LEU A 25 SER A 26 13 -124.31 REMARK 500 LEU A 25 SER A 26 15 -122.61 REMARK 500 LEU A 25 SER A 26 16 -106.66 REMARK 500 LEU A 25 SER A 26 17 -124.39 REMARK 500 LEU A 25 SER A 26 18 -123.30 REMARK 500 ALA A 33 PRO A 34 18 149.19 REMARK 500 LEU A 25 SER A 26 20 -123.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 ARG A 67 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6280 RELATED DB: BMRB REMARK 900 RELATED ID: 2B7V RELATED DB: PDB DBREF 2B7T A 1 73 UNP P51400 RED1_RAT 74 146 SEQRES 1 A 73 PRO GLY PRO VAL LEU PRO LYS ASN ALA LEU MET GLN LEU SEQRES 2 A 73 ASN GLU ILE LYS PRO GLY LEU GLN TYR MET LEU LEU SER SEQRES 3 A 73 GLN THR GLY PRO VAL HIS ALA PRO LEU PHE VAL MET SER SEQRES 4 A 73 VAL GLU VAL ASN GLY GLN VAL PHE GLU GLY SER GLY PRO SEQRES 5 A 73 THR LYS LYS LYS ALA LYS LEU HIS ALA ALA GLU LYS ALA SEQRES 6 A 73 LEU ARG SER PHE VAL GLN PHE PRO HELIX 1 1 PRO A 6 LYS A 17 1 12 HELIX 2 2 THR A 53 GLN A 71 1 19 SHEET 1 A 3 GLN A 21 THR A 28 0 SHEET 2 A 3 LEU A 35 GLU A 41 -1 O VAL A 37 N LEU A 25 SHEET 3 A 3 VAL A 46 GLY A 51 -1 O GLY A 51 N PHE A 36 CISPEP 1 GLY A 2 PRO A 3 1 -1.90 CISPEP 2 PHE A 72 PRO A 73 1 -4.40 CISPEP 3 GLY A 2 PRO A 3 3 -6.31 CISPEP 4 PRO A 3 VAL A 4 4 -1.02 CISPEP 5 PRO A 1 GLY A 2 5 -1.54 CISPEP 6 PHE A 72 PRO A 73 5 -17.88 CISPEP 7 PHE A 72 PRO A 73 6 2.65 CISPEP 8 GLY A 2 PRO A 3 7 8.03 CISPEP 9 PHE A 72 PRO A 73 7 -7.94 CISPEP 10 GLY A 2 PRO A 3 8 -6.17 CISPEP 11 PHE A 72 PRO A 73 8 -6.00 CISPEP 12 PHE A 72 PRO A 73 9 -3.10 CISPEP 13 GLY A 2 PRO A 3 10 -1.32 CISPEP 14 SER A 26 GLN A 27 10 2.08 CISPEP 15 PHE A 72 PRO A 73 10 -16.26 CISPEP 16 PHE A 72 PRO A 73 11 -10.05 CISPEP 17 PRO A 1 GLY A 2 12 -1.15 CISPEP 18 GLY A 2 PRO A 3 12 -12.42 CISPEP 19 LEU A 5 PRO A 6 13 0.21 CISPEP 20 PHE A 72 PRO A 73 14 -1.87 CISPEP 21 PRO A 1 GLY A 2 15 0.43 CISPEP 22 PHE A 72 PRO A 73 15 -16.32 CISPEP 23 PRO A 3 VAL A 4 16 21.74 CISPEP 24 PHE A 72 PRO A 73 17 -0.87 CISPEP 25 PRO A 1 GLY A 2 18 -0.33 CISPEP 26 PHE A 72 PRO A 73 18 10.68 CISPEP 27 LEU A 5 PRO A 6 19 -22.83 CISPEP 28 SER A 26 GLN A 27 19 -4.31 CISPEP 29 PHE A 72 PRO A 73 19 1.30 CISPEP 30 PRO A 1 GLY A 2 20 -1.67 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000