PDB Short entry for 2LTO HEADER TRANSCRIPTION/TRANSFERASE 30-MAY-12 2LTO TITLE TDRD3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TUDOR DOMAIN RESIDUES 554-608; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 1804-1816; COMPND 10 SYNONYM: RNA POLYMERASE II SUBUNIT B1, DNA-DIRECTED RNA POLYMERASE II COMPND 11 SUBUNIT A, DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT, RNA- COMPND 12 DIRECTED RNA POLYMERASE II SUBUNIT RPB1; COMPND 13 EC: 2.7.7.6, 2.7.7.48; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TDRD3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET22B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS ADMA, TRANSCRIPTION-TRANSFERASE COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SIKORSKY REVDAT 3 15-NOV-23 2LTO 1 REMARK SEQADV SEQRES LINK REVDAT 3 2 1 ATOM REVDAT 2 15-JUN-16 2LTO 1 HETATM MODRES REMARK REVDAT 1 16-JAN-13 2LTO 0 JRNL AUTH T.SIKORSKY,F.HOBOR,E.KRIZANOVA,J.PASULKA,K.KUBICEK,R.STEFL JRNL TITL RECOGNITION OF ASYMMETRICALLY DIMETHYLATED ARGININE BY JRNL TITL 2 TDRD3. JRNL REF NUCLEIC ACIDS RES. V. 40 11748 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 23066109 JRNL DOI 10.1093/NAR/GKS929 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, AMBER REMARK 3 AUTHORS : GODDARD (SPARKY), CASE, DARDEN, CHEATHAM III, REMARK 3 SIMMERLING, WANG, DUKE, LUO, AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LTO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000102819. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.7 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN_1, 50 MM SODIUM REMARK 210 PHOSPHATE, 10 MM BETA- REMARK 210 MERCAPTOETHANOL, 150 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HBHA(CO)NH; REMARK 210 3D HNCA; 3D CBCA(CO)NH; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE 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 : 20 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 574 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 ILE A 608 CA - CB - CG2 ANGL. DEV. = 12.2 DEGREES REMARK 500 3 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 TYR A 597 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 5 TYR B 618 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 6 ARG A 574 NH1 - CZ - NH2 ANGL. DEV. = -7.9 DEGREES REMARK 500 6 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 6 TYR A 597 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 7 ARG A 574 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 8 TYR A 573 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 11 TYR A 597 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 12 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 13 MET A 553 CG - SD - CE ANGL. DEV. = -9.9 DEGREES REMARK 500 14 TYR A 566 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 14 TYR A 573 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 14 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 TYR B 611 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 15 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 17 TYR A 597 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 17 TYR A 597 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 17 TYR B 611 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 18 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 20 ARG A 574 NE - CZ - NH1 ANGL. DEV. = 5.1 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 ALA A 579 108.19 -161.82 REMARK 500 1 HIS A 581 -0.92 -156.59 REMARK 500 1 SER A 583 12.65 -142.35 REMARK 500 1 SER B 614 -12.05 -150.82 REMARK 500 1 DA2 B 617 -48.24 56.52 REMARK 500 2 LEU A 580 62.13 -119.55 REMARK 500 2 HIS A 581 -33.69 -167.73 REMARK 500 2 SER A 582 -6.92 -57.67 REMARK 500 2 PHE A 591 109.31 -44.85 REMARK 500 2 TYR A 594 -34.34 -130.25 REMARK 500 2 SER B 612 -28.72 -171.00 REMARK 500 2 SER B 614 29.69 -152.38 REMARK 500 2 SER B 615 53.98 32.44 REMARK 500 2 DA2 B 617 154.08 -49.89 REMARK 500 2 THR B 619 71.14 -157.86 REMARK 500 2 SER B 622 -43.54 -160.74 REMARK 500 3 LYS A 554 -25.28 -153.07 REMARK 500 3 VAL A 577 119.09 -35.87 REMARK 500 3 ALA A 579 103.71 -169.31 REMARK 500 3 SER A 583 -19.62 -169.93 REMARK 500 3 ASP A 593 24.60 -140.34 REMARK 500 3 TYR A 594 -22.19 -152.91 REMARK 500 3 SER B 612 72.32 49.16 REMARK 500 3 TYR B 618 23.92 -59.96 REMARK 500 3 PRO B 620 151.37 -44.09 REMARK 500 4 LYS A 554 -38.01 -134.19 REMARK 500 4 LEU A 565 93.76 -64.92 REMARK 500 4 ALA A 579 103.90 -164.92 REMARK 500 4 SER A 583 -9.32 -56.30 REMARK 500 4 MET A 585 -37.27 -142.43 REMARK 500 4 LEU A 609 15.93 -155.46 REMARK 500 4 SER B 615 -50.23 124.12 REMARK 500 4 DA2 B 617 -178.26 -62.49 REMARK 500 4 TYR B 618 156.83 -47.16 REMARK 500 4 GLN B 621 -14.10 -156.12 REMARK 500 5 MET A 555 55.21 -173.15 REMARK 500 5 ALA A 579 99.70 -163.99 REMARK 500 5 LEU A 580 76.97 -115.25 REMARK 500 5 SER A 583 2.79 -58.61 REMARK 500 5 DA2 B 617 14.67 -144.08 REMARK 500 5 GLN B 621 42.39 37.14 REMARK 500 5 SER B 622 166.64 58.25 REMARK 500 6 TRP A 567 -37.75 -134.72 REMARK 500 6 ALA A 579 105.02 -161.11 REMARK 500 6 LEU A 609 -37.36 -134.83 REMARK 500 6 SER B 612 76.29 30.33 REMARK 500 6 SER B 615 73.45 -161.06 REMARK 500 6 DA2 B 617 -24.49 -141.95 REMARK 500 6 THR B 619 142.47 64.00 REMARK 500 6 PRO B 620 108.57 -54.36 REMARK 500 REMARK 500 THIS ENTRY HAS 146 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 574 0.09 SIDE CHAIN REMARK 500 13 TYR B 618 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18490 RELATED DB: BMRB DBREF 2LTO A 554 608 UNP Q9H7E2 TDRD3_HUMAN 554 608 DBREF 2LTO B 611 623 UNP P24928 RPB1_HUMAN 1804 1816 SEQADV 2LTO MET A 553 UNP Q9H7E2 EXPRESSION TAG SEQADV 2LTO LEU A 609 UNP Q9H7E2 EXPRESSION TAG SEQADV 2LTO GLU A 610 UNP Q9H7E2 EXPRESSION TAG SEQRES 1 A 58 MET LYS MET TRP LYS PRO GLY ASP GLU CYS PHE ALA LEU SEQRES 2 A 58 TYR TRP GLU ASP ASN LYS PHE TYR ARG ALA GLU VAL GLU SEQRES 3 A 58 ALA LEU HIS SER SER GLY MET THR ALA VAL VAL LYS PHE SEQRES 4 A 58 ILE ASP TYR GLY ASN TYR GLU GLU VAL LEU LEU SER ASN SEQRES 5 A 58 ILE LYS PRO ILE LEU GLU SEQRES 1 B 13 TYR SER PRO SER SER PRO DA2 TYR THR PRO GLN SER PRO MODRES 2LTO DA2 B 617 ARG NG,NG-DIMETHYL-L-ARGININE HET DA2 B 617 30 HETNAM DA2 NG,NG-DIMETHYL-L-ARGININE HETSYN DA2 ADMA FORMUL 2 DA2 C8 H18 N4 O2 SHEET 1 A 5 TYR A 597 LEU A 601 0 SHEET 2 A 5 THR A 586 PHE A 591 -1 N ALA A 587 O VAL A 600 SHEET 3 A 5 PHE A 572 ALA A 579 -1 N GLU A 576 O LYS A 590 SHEET 4 A 5 ASP A 560 LEU A 565 -1 N CYS A 562 O ALA A 575 SHEET 5 A 5 ILE A 605 LYS A 606 -1 O LYS A 606 N PHE A 563 LINK C PRO B 616 N DA2 B 617 1555 1555 1.34 LINK C DA2 B 617 N TYR B 618 1555 1555 1.35 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