HEADER REPLICATION 08-SEP-12 4B9W TITLE STRUCTURE OF EXTENDED TUDOR DOMAIN TD3 FROM MOUSE TDRD1 IN COMPLEX TITLE 2 WITH MILI PEPTIDE CONTAINING DIMETHYLARGININE 45. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EXTENDED TUDOR DOMAIN TD3, RESIDUES 692-892; COMPND 5 SYNONYM: TDRD1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PIWI-LIKE PROTEIN 2; COMPND 9 CHAIN: P, S; COMPND 10 FRAGMENT: N-TERMINAL PEPTIDE CONTAINING METHYLATED ARG45, RESIDUES COMPND 11 38-50; COMPND 12 SYNONYM: MILI; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: ARG45 IS SYMMETRICALLY DIMETHYLATED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PETM11; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 14 ORGANISM_TAXID: 10090 KEYWDS REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR N.MATHIOUDAKIS,A.PALENCIA,J.KADLEC,A.ROUND,K.TRIPSIANES,M.SATTLER, AUTHOR 2 R.S.PILLAI,S.CUSACK REVDAT 4 13-NOV-24 4B9W 1 REMARK SHEET LINK REVDAT 3 10-APR-19 4B9W 1 JRNL REMARK DBREF LINK REVDAT 2 31-OCT-12 4B9W 1 JRNL REVDAT 1 17-OCT-12 4B9W 0 JRNL AUTH N.MATHIOUDAKIS,A.PALENCIA,J.KADLEC,A.ROUND,K.TRIPSIANES, JRNL AUTH 2 M.SATTLER,R.S.PILLAI,S.CUSACK JRNL TITL THE MULTIPLE TUDOR DOMAIN-CONTAINING PROTEIN TDRD1 IS A JRNL TITL 2 MOLECULAR SCAFFOLD FOR MOUSE PIWI PROTEINS AND PIRNA JRNL TITL 3 BIOGENESIS FACTORS. JRNL REF RNA V. 18 2056 2012 JRNL REFN ESSN 1469-9001 JRNL PMID 22996915 JRNL DOI 10.1261/RNA.034181.112 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0116 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 24480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1275 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1790 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3207 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 186 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : 0.08000 REMARK 3 B13 (A**2) : 0.07000 REMARK 3 B23 (A**2) : 0.10000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.268 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.230 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.166 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.314 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.859 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3304 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2193 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4492 ; 1.377 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5360 ; 0.861 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 6.684 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;34.436 ;24.803 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 534 ;14.557 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.833 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 503 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3660 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 672 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4B9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1290054012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25755 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.550 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP, RESOLVE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN:PEPTIDE 1:5 RATIO, 0.2 M REMARK 280 AMMONIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.5, 30 % PEG8000, REMARK 280 0.01 M MAGNESIUM ACETATE TETRAHYDRATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P, S 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 692 REMARK 465 PRO A 693 REMARK 465 ALA A 694 REMARK 465 GLU A 695 REMARK 465 ALA A 696 REMARK 465 GLY B 692 REMARK 465 PRO B 693 REMARK 465 ALA B 694 REMARK 465 GLU B 695 REMARK 465 ALA B 696 REMARK 465 LYS B 750 REMARK 465 PRO B 751 REMARK 465 PRO B 752 REMARK 465 ASN B 753 REMARK 465 GLY B 754 REMARK 465 GLY P 38 REMARK 465 ARG P 39 REMARK 465 ALA P 40 REMARK 465 GLY P 41 REMARK 465 PRO P 42 REMARK 465 GLY S 38 REMARK 465 ARG S 39 REMARK 465 ALA S 40 REMARK 465 GLY S 41 REMARK 465 PRO S 42 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OE2 GLU A 722 O HOH A 2021 2.08 REMARK 500 O HOH A 2009 O HOH A 2035 2.12 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 ARG A 841 NE - CZ - NH1 ANGL. DEV. = 3.4 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 GLU A 722 93.23 -160.58 REMARK 500 TYR A 794 -37.93 -137.90 REMARK 500 ASN A 831 -124.91 -102.04 REMARK 500 GLU B 722 97.85 -163.49 REMARK 500 TYR B 794 -37.06 -134.32 REMARK 500 ASN B 831 -109.36 -103.75 REMARK 500 ARG B 890 151.79 -48.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 GLYCEROL (GOL): FROM CRYOPROTECTANT REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1893 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1893 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4B9X RELATED DB: PDB REMARK 900 STRUCTURE OF EXTENDED TUDOR DOMAIN TD3 FROM MOUSE TDRD1 DBREF 4B9W A 692 892 UNP Q99MV1 TDRD1_MOUSE 692 892 DBREF 4B9W B 692 892 UNP Q99MV1 TDRD1_MOUSE 692 892 DBREF 4B9W P 38 50 UNP Q8CDG1 PIWL2_MOUSE 38 50 DBREF 4B9W S 38 50 UNP Q8CDG1 PIWL2_MOUSE 38 50 SEQRES 1 A 201 GLY PRO ALA GLU ALA LEU GLU TRP THR TRP VAL GLU PHE SEQRES 2 A 201 THR VAL ASP GLU THR VAL ASP VAL VAL VAL CYS MET MET SEQRES 3 A 201 TYR SER PRO GLY GLU PHE TYR CYS HIS PHE LEU LYS ASP SEQRES 4 A 201 ASP ALA LEU GLU LYS LEU ASP ASP LEU ASN GLN SER LEU SEQRES 5 A 201 ALA ASP TYR CYS ALA GLN LYS PRO PRO ASN GLY PHE LYS SEQRES 6 A 201 ALA GLU ILE GLY ARG PRO CYS CYS ALA PHE PHE SER GLY SEQRES 7 A 201 ASP GLY ASN TRP TYR ARG ALA LEU VAL LYS GLU ILE LEU SEQRES 8 A 201 PRO SER GLY ASN VAL LYS VAL HIS PHE VAL ASP TYR GLY SEQRES 9 A 201 ASN VAL GLU GLU VAL THR THR ASP GLN LEU GLN ALA ILE SEQRES 10 A 201 LEU PRO GLN PHE LEU LEU LEU PRO PHE GLN GLY MET GLN SEQRES 11 A 201 CYS TRP LEU VAL ASP ILE GLN PRO PRO ASN LYS HIS TRP SEQRES 12 A 201 THR LYS GLU ALA THR ALA ARG PHE GLN ALA CYS VAL VAL SEQRES 13 A 201 GLY LEU LYS LEU GLN ALA ARG VAL VAL GLU ILE THR ALA SEQRES 14 A 201 ASN GLY VAL GLY VAL GLU LEU THR ASP LEU SER THR PRO SEQRES 15 A 201 TYR PRO LYS ILE ILE SER ASP VAL LEU ILE ARG GLU GLN SEQRES 16 A 201 LEU VAL LEU ARG CYS GLY SEQRES 1 B 201 GLY PRO ALA GLU ALA LEU GLU TRP THR TRP VAL GLU PHE SEQRES 2 B 201 THR VAL ASP GLU THR VAL ASP VAL VAL VAL CYS MET MET SEQRES 3 B 201 TYR SER PRO GLY GLU PHE TYR CYS HIS PHE LEU LYS ASP SEQRES 4 B 201 ASP ALA LEU GLU LYS LEU ASP ASP LEU ASN GLN SER LEU SEQRES 5 B 201 ALA ASP TYR CYS ALA GLN LYS PRO PRO ASN GLY PHE LYS SEQRES 6 B 201 ALA GLU ILE GLY ARG PRO CYS CYS ALA PHE PHE SER GLY SEQRES 7 B 201 ASP GLY ASN TRP TYR ARG ALA LEU VAL LYS GLU ILE LEU SEQRES 8 B 201 PRO SER GLY ASN VAL LYS VAL HIS PHE VAL ASP TYR GLY SEQRES 9 B 201 ASN VAL GLU GLU VAL THR THR ASP GLN LEU GLN ALA ILE SEQRES 10 B 201 LEU PRO GLN PHE LEU LEU LEU PRO PHE GLN GLY MET GLN SEQRES 11 B 201 CYS TRP LEU VAL ASP ILE GLN PRO PRO ASN LYS HIS TRP SEQRES 12 B 201 THR LYS GLU ALA THR ALA ARG PHE GLN ALA CYS VAL VAL SEQRES 13 B 201 GLY LEU LYS LEU GLN ALA ARG VAL VAL GLU ILE THR ALA SEQRES 14 B 201 ASN GLY VAL GLY VAL GLU LEU THR ASP LEU SER THR PRO SEQRES 15 B 201 TYR PRO LYS ILE ILE SER ASP VAL LEU ILE ARG GLU GLN SEQRES 16 B 201 LEU VAL LEU ARG CYS GLY SEQRES 1 P 13 GLY ARG ALA GLY PRO ALA GLY 2MR GLY LEU VAL PHE ARG SEQRES 1 S 13 GLY ARG ALA GLY PRO ALA GLY 2MR GLY LEU VAL PHE ARG MODRES 4B9W 2MR P 45 ARG N3, N4-DIMETHYLARGININE MODRES 4B9W 2MR S 45 ARG N3, N4-DIMETHYLARGININE HET 2MR P 45 13 HET 2MR S 45 13 HET GOL A1893 6 HET GOL B1893 6 HETNAM 2MR N3, N4-DIMETHYLARGININE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 2MR 2(C8 H18 N4 O2) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *186(H2 O) HELIX 1 1 ASP A 731 GLN A 749 1 19 HELIX 2 2 THR A 801 ASP A 803 5 3 HELIX 3 3 LEU A 809 LEU A 814 5 6 HELIX 4 4 THR A 835 VAL A 847 1 13 HELIX 5 5 ILE A 878 GLU A 885 1 8 HELIX 6 6 ASP B 731 ALA B 748 1 18 HELIX 7 7 THR B 801 ASP B 803 5 3 HELIX 8 8 LEU B 809 LEU B 814 5 6 HELIX 9 9 THR B 835 VAL B 847 1 13 HELIX 10 10 ILE B 878 GLU B 885 1 8 SHEET 1 AA 6 THR A 709 SER A 719 0 SHEET 2 AA 6 LEU A 851 THR A 859 -1 O LEU A 851 N VAL A 712 SHEET 3 AA 6 GLY A 862 ASP A 869 1 O GLY A 862 N THR A 859 SHEET 4 AA 6 MET A 820 LEU A 824 1 O GLN A 821 N VAL A 863 SHEET 5 AA 6 GLU A 722 PHE A 727 -1 O PHE A 723 N CYS A 822 SHEET 6 AA 6 THR A 709 SER A 719 0 SHEET 1 AB 5 VAL A 797 VAL A 800 0 SHEET 2 AB 5 VAL A 787 PHE A 791 -1 O VAL A 787 N VAL A 800 SHEET 3 AB 5 TRP A 773 ILE A 781 -1 O LEU A 777 N HIS A 790 SHEET 4 AB 5 PRO A 762 PHE A 766 -1 O CYS A 763 N ALA A 776 SHEET 5 AB 5 LEU A 805 ALA A 807 -1 O GLN A 806 N CYS A 764 SHEET 1 AC 2 ILE A 827 GLN A 828 0 SHEET 2 AC 2 LEU A 889 ARG A 890 -1 O LEU A 889 N GLN A 828 SHEET 1 BA 6 THR B 709 SER B 719 0 SHEET 2 BA 6 LEU B 851 ILE B 858 -1 O LEU B 851 N VAL B 712 SHEET 3 BA 6 VAL B 863 ASP B 869 1 O GLY B 864 N VAL B 856 SHEET 4 BA 6 MET B 820 LEU B 824 1 O GLN B 821 N VAL B 863 SHEET 5 BA 6 GLU B 722 PHE B 727 -1 O PHE B 723 N CYS B 822 SHEET 6 BA 6 THR B 709 SER B 719 0 SHEET 1 BB 5 VAL B 797 VAL B 800 0 SHEET 2 BB 5 VAL B 787 PHE B 791 -1 O VAL B 787 N VAL B 800 SHEET 3 BB 5 TRP B 773 ILE B 781 -1 O LEU B 777 N HIS B 790 SHEET 4 BB 5 PRO B 762 PHE B 766 -1 O CYS B 763 N ALA B 776 SHEET 5 BB 5 LEU B 805 GLN B 806 -1 O GLN B 806 N CYS B 764 SHEET 1 BC 2 ILE B 827 GLN B 828 0 SHEET 2 BC 2 LEU B 889 ARG B 890 -1 O LEU B 889 N GLN B 828 LINK C GLY P 44 N 2MR P 45 1555 1555 1.34 LINK C 2MR P 45 N GLY P 46 1555 1555 1.32 LINK C GLY S 44 N 2MR S 45 1555 1555 1.33 LINK C 2MR S 45 N GLY S 46 1555 1555 1.32 CISPEP 1 LYS A 750 PRO A 751 0 0.54 SITE 1 AC1 7 VAL B 714 CYS B 715 MET B 716 MET B 717 SITE 2 AC1 7 GLN B 843 2MR S 45 LEU S 47 SITE 1 AC2 5 CYS A 715 MET A 717 GLN A 843 2MR P 45 SITE 2 AC2 5 LEU P 47 CRYST1 39.940 53.960 60.790 93.69 98.56 111.68 P 1 2 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 0.025038 0.009954 0.005105 0.00000 SCALE2 0.000000 0.019943 0.002612 0.00000 SCALE3 0.000000 0.000000 0.016777 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.999988 -0.000511 0.004916 -0.21223 1 MTRIX2 2 -0.000503 -0.999998 -0.001670 70.61587 1 MTRIX3 2 0.004917 0.001667 -0.999987 95.13131 1