PDB Short entry for 2C5Z HEADER TRANSCRIPTION 03-NOV-05 2C5Z TITLE STRUCTURE AND CTD BINDING OF THE SET2 SRI DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SET DOMAIN PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SET2 RPB1 INTERACTING DOMAIN, RESIDUES 620-719; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES 1-4 IN THE CONSTRUCT USED FOR THE STRUCTURE COMPND 7 DETERMINATION ARE FROM THE EXPRESSION VECTOR. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; 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_PLASMID: PET 9D KEYWDS SRI DOMAIN, RNA POLYMERASE II, TRANSCRIPTION, CTD, SET2 HISTONE KEYWDS 2 METHYLTRANSFERASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.VOJNIC,B.SIMON,B.D.STRAHL,M.SATTLER,P.CRAMER REVDAT 4 09-MAY-18 2C5Z 1 JRNL REMARK REVDAT 3 24-FEB-09 2C5Z 1 VERSN REVDAT 2 18-JAN-06 2C5Z 1 JRNL REVDAT 1 14-NOV-05 2C5Z 0 JRNL AUTH E.VOJNIC,B.SIMON,B.D.STRAHL,M.SATTLER,P.CRAMER JRNL TITL STRUCTURE AND CARBOXYL-TERMINAL DOMAIN (CTD) BINDING OF THE JRNL TITL 2 SET2 SRI DOMAIN THAT COUPLES HISTONE H3 LYS36 METHYLATION TO JRNL TITL 3 TRANSCRIPTION. JRNL REF J. BIOL. CHEM. V. 281 13 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16286474 JRNL DOI 10.1074/JBC.C500423200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, ARIA 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE NMR ENSEMBLE HAS BEEN REFINED IN A REMARK 3 SHELL OF WATER MOLECULES. REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE AND LINGE ET AL. REMARK 4 REMARK 4 2C5Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026244. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 292.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSHATE, 200 MM REMARK 210 SODIUM CHLORIDE REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 0.4-1MM 15N OR 15N/13C LABELLED REMARK 210 PROTEIN, 90% WATER/ 10% D2O OR REMARK 210 100 % D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW REMARK 210 METHOD USED : ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 3D_15N-SEPARATED_NOESY, 3D_13C-SEPARATED_NOESY, 3D_13C REMARK 210 EDITED NOESY, 3D_15N EDITED NOESY, HNHA, 2 D NOESY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 616 REMARK 465 ALA A 617 REMARK 465 MET A 618 REMARK 465 GLY A 619 REMARK 465 LYS A 620 REMARK 465 THR A 621 REMARK 465 LEU A 715 REMARK 465 GLY A 716 REMARK 465 LEU A 717 REMARK 465 SER A 718 REMARK 465 SER A 719 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 HZ2 TRP A 632 HD2 ARG A 680 1.23 REMARK 500 HZ3 LYS A 663 OD1 ASP A 664 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 6 PHE A 636 CE1 PHE A 636 CZ -0.123 REMARK 500 6 PHE A 636 CZ PHE A 636 CE2 0.134 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 LYS A 646 74.00 -152.63 REMARK 500 1 LEU A 686 97.64 -64.22 REMARK 500 2 SER A 623 42.36 -84.44 REMARK 500 2 LYS A 646 80.00 -165.06 REMARK 500 3 LYS A 646 72.31 -170.30 REMARK 500 4 SER A 623 18.65 59.44 REMARK 500 4 LYS A 646 84.06 -165.68 REMARK 500 4 LEU A 686 95.23 -69.37 REMARK 500 5 LYS A 646 73.20 -175.52 REMARK 500 5 PRO A 648 -19.83 -47.40 REMARK 500 6 LYS A 646 85.42 -164.47 REMARK 500 7 LYS A 646 65.45 -179.16 REMARK 500 7 ASP A 684 -73.89 -49.69 REMARK 500 7 LEU A 686 97.13 -62.82 REMARK 500 8 LYS A 646 80.24 -167.14 REMARK 500 9 LYS A 646 81.96 -173.28 REMARK 500 10 LYS A 646 70.94 -172.19 REMARK 500 10 ASP A 684 -71.98 -58.21 REMARK 500 10 LEU A 686 95.49 -63.95 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 4 PHE A 653 0.06 SIDE CHAIN REMARK 500 7 PHE A 639 0.07 SIDE CHAIN REMARK 500 10 PHE A 653 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E0N RELATED DB: PDB REMARK 900 YJQ8WW DOMAIN FROM SACCHAROMYCES CEREVISAE REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1-4 IN THE CONSTRUCT USED FOR THE STRUCTURE REMARK 999 DETERMINATION ARE FROM THE EXPRESSION VECTOR. DBREF 2C5Z A 616 619 PDB 2C5Z 2C5Z 616 619 DBREF 2C5Z A 620 719 UNP P46995 SET2_YEAST 620 719 SEQRES 1 A 104 GLY ALA MET GLY LYS THR VAL SER GLN SER GLN ARG LEU SEQRES 2 A 104 GLU HIS ASN TRP ASN LYS PHE PHE ALA SER PHE VAL PRO SEQRES 3 A 104 ASN LEU ILE LYS LYS ASN PRO GLN SER LYS GLN PHE ASP SEQRES 4 A 104 HIS GLU ASN ILE LYS GLN CYS ALA LYS ASP ILE VAL LYS SEQRES 5 A 104 ILE LEU THR THR LYS GLU LEU LYS LYS ASP SER SER ARG SEQRES 6 A 104 ALA PRO PRO ASP ASP LEU THR LYS GLY LYS ARG HIS LYS SEQRES 7 A 104 VAL LYS GLU PHE ILE ASN SER TYR MET ASP LYS ILE ILE SEQRES 8 A 104 LEU LYS LYS LYS GLN LYS LYS ALA LEU GLY LEU SER SER HELIX 1 1 SER A 623 LYS A 646 1 24 HELIX 2 2 ASP A 654 ASP A 677 1 24 HELIX 3 3 THR A 687 LYS A 713 1 27 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