HEADER RNA BINDING PROTEIN 06-AUG-11 2LH9 TITLE NMR STRUCTURE OF THE FIRST LOTUS DOMAIN OF TUDOR DOMAIN-CONTAINING TITLE 2 PROTEIN 7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR DOMAIN-CONTAINING PROTEIN 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 1-76; 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PTEV KEYWDS RNA BINDING DOMAIN, RIBONUCLEOPROTEIN, RNA GRANULE COMPONENT, RNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.CUI,M.BOTUYAN,G.MER REVDAT 1 08-AUG-12 2LH9 0 JRNL AUTH G.CUI,M.BOTUYAN,G.MER JRNL TITL NMR STRUCTURE OF TUDOR 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 : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-11. REMARK 100 THE RCSB ID CODE IS RCSB102383. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.3 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-100% 15N] PROTEIN, 50 REMARK 210 MM SODIUM ACETATE, 90% H2O/10% REMARK 210 D2O; 1.5 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 50 MM SODIUM REMARK 210 ACETATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 HBHA(CO)NH; 3D CCH-TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 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 : CYANA, SANE, NMRVIEW 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 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: 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 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 3 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 8 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 10 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 11 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 13 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 18 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 19 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 20 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.1 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 PRO A 73 39.52 -84.89 REMARK 500 1 VAL A 108 -27.37 -142.98 REMARK 500 2 HIS A 51 63.58 -102.51 REMARK 500 2 PRO A 73 47.70 -81.15 REMARK 500 2 VAL A 108 -29.61 -140.91 REMARK 500 3 HIS A 51 64.78 -100.84 REMARK 500 3 PRO A 73 40.33 -85.33 REMARK 500 3 VAL A 108 -28.80 -143.37 REMARK 500 4 HIS A 51 64.99 -105.48 REMARK 500 4 PRO A 73 46.61 -81.91 REMARK 500 5 HIS A 51 66.09 -100.34 REMARK 500 5 PRO A 73 46.93 -80.87 REMARK 500 5 VAL A 108 -36.15 -139.78 REMARK 500 6 HIS A 51 64.10 -103.69 REMARK 500 6 PRO A 73 41.56 -83.30 REMARK 500 6 VAL A 108 -28.74 -143.21 REMARK 500 7 PRO A 73 40.52 -85.07 REMARK 500 7 VAL A 108 -28.88 -143.16 REMARK 500 8 HIS A 51 64.70 -108.59 REMARK 500 8 PRO A 73 32.30 -83.58 REMARK 500 8 VAL A 108 -26.73 -144.26 REMARK 500 9 PRO A 73 40.92 -85.49 REMARK 500 10 PRO A 73 32.87 -84.58 REMARK 500 10 VAL A 108 -30.67 -142.18 REMARK 500 11 HIS A 51 63.90 -104.85 REMARK 500 11 PRO A 73 40.88 -84.74 REMARK 500 11 VAL A 108 -29.75 -140.81 REMARK 500 12 HIS A 51 64.28 -110.64 REMARK 500 12 PRO A 73 41.28 -85.11 REMARK 500 12 VAL A 108 -28.09 -141.76 REMARK 500 13 PRO A 73 37.21 -84.02 REMARK 500 13 VAL A 108 -28.86 -140.88 REMARK 500 14 HIS A 51 64.34 -101.87 REMARK 500 14 PRO A 73 45.32 -80.96 REMARK 500 14 VAL A 108 -30.44 -140.69 REMARK 500 15 HIS A 51 63.90 -102.97 REMARK 500 15 PRO A 73 46.96 -81.45 REMARK 500 15 VAL A 108 -27.88 -140.81 REMARK 500 16 HIS A 51 63.94 -102.87 REMARK 500 16 PRO A 73 40.28 -84.50 REMARK 500 16 VAL A 108 -34.56 -139.29 REMARK 500 17 HIS A 51 63.37 -114.13 REMARK 500 17 PRO A 73 48.01 -81.95 REMARK 500 18 HIS A 51 64.52 -102.21 REMARK 500 18 PRO A 73 46.40 -80.96 REMARK 500 18 VAL A 108 -27.73 -143.12 REMARK 500 19 HIS A 51 64.14 -100.26 REMARK 500 19 PRO A 73 42.00 -83.70 REMARK 500 19 VAL A 108 -29.27 -141.60 REMARK 500 20 HIS A 51 64.62 -109.26 REMARK 500 REMARK 500 THIS ENTRY HAS 52 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 5 ARG A 94 0.08 SIDE CHAIN REMARK 500 11 ARG A 94 0.08 SIDE CHAIN REMARK 500 14 ARG A 94 0.08 SIDE CHAIN REMARK 500 15 ARG A 45 0.08 SIDE CHAIN REMARK 500 16 ARG A 94 0.08 SIDE CHAIN REMARK 500 20 ARG A 94 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 2 LEU A 57 24.3 L L OUTSIDE RANGE REMARK 500 3 LEU A 57 24.5 L L OUTSIDE RANGE REMARK 500 4 LEU A 57 24.1 L L OUTSIDE RANGE REMARK 500 5 LEU A 57 24.6 L L OUTSIDE RANGE REMARK 500 6 LEU A 57 24.4 L L OUTSIDE RANGE REMARK 500 7 LEU A 57 24.7 L L OUTSIDE RANGE REMARK 500 8 LEU A 57 24.2 L L OUTSIDE RANGE REMARK 500 9 LEU A 57 24.4 L L OUTSIDE RANGE REMARK 500 10 LEU A 57 24.6 L L OUTSIDE RANGE REMARK 500 11 LEU A 57 24.5 L L OUTSIDE RANGE REMARK 500 12 LEU A 57 24.5 L L OUTSIDE RANGE REMARK 500 13 LEU A 57 24.3 L L OUTSIDE RANGE REMARK 500 14 LEU A 57 24.2 L L OUTSIDE RANGE REMARK 500 15 LEU A 57 24.2 L L OUTSIDE RANGE REMARK 500 16 LEU A 57 24.4 L L OUTSIDE RANGE REMARK 500 17 LEU A 57 24.2 L L OUTSIDE RANGE REMARK 500 18 LEU A 57 24.8 L L OUTSIDE RANGE REMARK 500 19 LEU A 57 24.2 L L OUTSIDE RANGE REMARK 500 20 LEU A 57 24.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17835 RELATED DB: BMRB DBREF 2LH9 A 34 109 UNP Q8K1H1 TDRD7_MOUSE 1 76 SEQADV 2LH9 GLY A -2 UNP Q8K1H1 EXPRESSION TAG SEQADV 2LH9 HIS A -1 UNP Q8K1H1 EXPRESSION TAG SEQRES 1 A 78 GLY HIS MET LEU GLU ALA ASP LEU VAL SER LYS MET LEU SEQRES 2 A 78 ARG ALA VAL LEU GLN SER HIS LYS ASN GLY ILE VAL LEU SEQRES 3 A 78 PRO ARG LEU GLN GLY GLU TYR ARG SER LEU THR GLY ASP SEQRES 4 A 78 TRP ILE PRO PHE LYS GLN LEU GLY TYR PRO THR LEU GLU SEQRES 5 A 78 ALA TYR LEU ARG SER VAL PRO ALA VAL VAL ARG ILE GLU SEQRES 6 A 78 ALA SER ARG SER GLY GLU ILE VAL CYS TYR ALA VAL ALA HELIX 1 1 LEU A 35 HIS A 51 1 17 HELIX 2 2 LEU A 57 GLY A 69 1 13 HELIX 3 3 PRO A 73 GLY A 78 1 6 HELIX 4 4 THR A 81 SER A 88 1 8 SHEET 1 A 3 ILE A 55 VAL A 56 0 SHEET 2 A 3 ILE A 103 ALA A 107 -1 O CYS A 105 N ILE A 55 SHEET 3 A 3 VAL A 93 ALA A 97 -1 N ARG A 94 O TYR A 106 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