HEADER RNA BINDING PROTEIN 10-SEP-12 2LY2 TITLE NMR STRUCTURE OF THE SECOND AND THIRD LOTUS DOMAINS OF TUDOR DOMAIN- TITLE 2 CONTAINING PROTEIN 7 (NMR ENSEMBLE OVERLAY FOR LOTUS #3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR DOMAIN-CONTAINING PROTEIN 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LOTUS DOMAINS 2 AND 3; COMPND 5 SYNONYM: PCTAIRE2-BINDING PROTEIN, TUDOR REPEAT ASSOCIATOR WITH COMPND 6 PCTAIRE 2, TRAP; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TDRD7, PCTAIRE2BP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTEV KEYWDS TDRD7, LOTUS DOMAIN, OST-HTH DOMAIN, RNA BINDING DOMAIN, GERMINAL KEYWDS 2 GRANULES, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.CUI,M.BOTUYAN,G.MER REVDAT 2 01-MAY-24 2LY2 1 REMARK SEQADV REVDAT 1 11-SEP-13 2LY2 0 JRNL AUTH G.CUI,M.BOTUYAN,G.MER JRNL TITL NMR STRUCTURE OF THE SECOND AND THIRD LOTUS DOMAINS OF TUDOR JRNL TITL 2 DOMAIN-CONTAINING PROTEIN 7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, AMBER REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CASE, DARDEN, CHEATHAM, III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000102975. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.26 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 TDRD7 (LOTUS1-LOTUS2), 90 % H2O, REMARK 210 10 % D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D H(CCO)NH; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, XWINNMR, SANE, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HG SER A 277 OD2 ASP A 317 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 1 PHE A 386 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 PHE A 386 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 4 PHE A 386 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 4 PHE A 386 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 PHE A 386 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 15 PHE A 386 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 16 PHE A 386 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 17 PHE A 386 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 19 PHE A 386 CB - CG - CD2 ANGL. DEV. = -4.7 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 HIS A -1 -64.94 -159.20 REMARK 500 1 ASN A 271 -58.07 58.17 REMARK 500 1 LYS A 310 72.61 -115.10 REMARK 500 1 GLN A 316 11.65 -145.86 REMARK 500 1 ALA A 323 4.23 -55.36 REMARK 500 1 LEU A 329 42.25 -160.10 REMARK 500 1 GLN A 333 11.26 -146.84 REMARK 500 1 LEU A 339 70.20 23.58 REMARK 500 1 PRO A 360 166.01 -49.77 REMARK 500 1 SER A 415 -12.26 66.70 REMARK 500 1 LEU A 427 63.88 36.30 REMARK 500 1 LEU A 429 70.08 -151.87 REMARK 500 2 HIS A 270 52.50 -114.57 REMARK 500 2 LYS A 310 68.67 -119.40 REMARK 500 2 ALA A 323 -2.92 -58.90 REMARK 500 2 ASP A 334 43.08 -140.95 REMARK 500 2 PRO A 335 39.26 -75.33 REMARK 500 2 GLU A 336 -45.72 -142.21 REMARK 500 2 LYS A 337 -63.75 40.42 REMARK 500 2 LEU A 339 56.79 31.41 REMARK 500 2 VAL A 358 105.76 -57.33 REMARK 500 2 SER A 415 -13.63 69.58 REMARK 500 2 LEU A 427 64.25 31.42 REMARK 500 3 HIS A 270 52.64 -107.20 REMARK 500 3 PRO A 311 162.80 -49.42 REMARK 500 3 ALA A 323 4.90 -52.02 REMARK 500 3 GLU A 326 -6.04 49.99 REMARK 500 3 LEU A 339 59.50 27.86 REMARK 500 3 VAL A 350 78.23 45.73 REMARK 500 3 SER A 415 -16.19 66.14 REMARK 500 3 LEU A 427 60.76 38.36 REMARK 500 3 PRO A 430 34.97 -75.83 REMARK 500 4 TRP A 302 79.47 -102.14 REMARK 500 4 LYS A 310 65.09 -117.53 REMARK 500 4 ARG A 325 24.89 -140.14 REMARK 500 4 GLN A 333 41.82 -76.68 REMARK 500 4 LEU A 339 61.34 34.13 REMARK 500 4 PRO A 341 150.61 -49.13 REMARK 500 4 SER A 355 84.34 59.00 REMARK 500 4 MET A 359 70.39 -119.78 REMARK 500 4 SER A 415 -12.59 66.52 REMARK 500 4 LEU A 427 65.20 35.54 REMARK 500 4 PRO A 430 13.55 -62.36 REMARK 500 5 HIS A 270 53.21 -118.62 REMARK 500 5 CYS A 312 45.98 -85.49 REMARK 500 5 ARG A 325 17.80 -146.72 REMARK 500 5 ASP A 334 70.64 40.51 REMARK 500 5 GLU A 336 7.54 -159.00 REMARK 500 5 GLU A 338 -32.65 -131.04 REMARK 500 5 LEU A 339 54.61 27.84 REMARK 500 REMARK 500 THIS ENTRY HAS 198 RAMACHANDRAN OUTLIERS. 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 1 PHE A 394 0.09 SIDE CHAIN REMARK 500 11 PHE A 394 0.10 SIDE CHAIN REMARK 500 14 PHE A 394 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18211 RELATED DB: BMRB REMARK 900 RELATED ID: 2LY1 RELATED DB: PDB DBREF 2LY2 A 256 433 UNP Q8K1H1 TDRD7_MOUSE 223 400 SEQADV 2LY2 GLY A -2 UNP Q8K1H1 EXPRESSION TAG SEQADV 2LY2 HIS A -1 UNP Q8K1H1 EXPRESSION TAG SEQRES 1 A 180 GLY HIS MET ASP GLU VAL GLN ASN ARG ILE LYS GLU ILE SEQRES 2 A 180 LEU ASP LYS HIS ASN ASN GLY ILE TRP ILE SER LYS LEU SEQRES 3 A 180 PRO HIS PHE TYR LYS GLU PHE TYR LYS GLU ASP LEU ASN SEQRES 4 A 180 GLN GLY VAL LEU GLN GLN PHE GLU HIS TRP PRO HIS ILE SEQRES 5 A 180 CYS THR VAL GLU LYS PRO CYS GLY GLY GLY GLN ASP SER SEQRES 6 A 180 LEU LEU TYR PRO ALA ARG ARG GLU GLN PRO LEU LYS SER SEQRES 7 A 180 ASP GLN ASP PRO GLU LYS GLU LEU PRO PRO PRO PRO PRO SEQRES 8 A 180 ALA PRO LYS GLN GLU VAL PRO SER GLN GLY SER PRO ALA SEQRES 9 A 180 VAL MET PRO ASP VAL LYS GLU LYS VAL ALA GLU LEU LEU SEQRES 10 A 180 GLY LYS TYR SER SER GLY LEU TRP ALA SER ALA LEU PRO SEQRES 11 A 180 LYS ALA PHE GLU ASP MET TYR LYS VAL LYS PHE PRO GLU SEQRES 12 A 180 ASP ALA LEU LYS ASN LEU ALA SER LEU SER ASP VAL CYS SEQRES 13 A 180 THR ILE ASN TYR ILE SER GLY ASN THR GLN LYS ALA ILE SEQRES 14 A 180 LEU TYR ALA LYS LEU PRO LEU PRO THR ASP LYS HELIX 1 1 HIS A -1 ASN A 271 1 17 HELIX 2 2 LYS A 278 LYS A 288 1 11 HELIX 3 3 ASN A 292 TRP A 302 1 11 HELIX 4 4 ARG A 324 GLU A 326 5 3 HELIX 5 5 GLN A 333 GLU A 338 1 6 HELIX 6 6 ALA A 345 GLU A 349 5 5 HELIX 7 7 PRO A 360 LYS A 372 1 13 HELIX 8 8 SER A 380 LYS A 391 1 12 HELIX 9 9 PRO A 395 LYS A 400 1 6 HELIX 10 10 ASN A 401 VAL A 408 1 8 SHEET 1 A 3 ILE A 274 TRP A 275 0 SHEET 2 A 3 LEU A 319 PRO A 322 -1 O LEU A 320 N ILE A 274 SHEET 3 A 3 CYS A 306 GLU A 309 -1 N THR A 307 O TYR A 321 SHEET 1 B 3 LEU A 377 TRP A 378 0 SHEET 2 B 3 LYS A 420 ALA A 425 -1 O LEU A 423 N LEU A 377 SHEET 3 B 3 CYS A 409 ILE A 414 -1 N ASN A 412 O ILE A 422 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 MODEL 1