HEADER TRANSCRIPTION 02-APR-15 2N1I TITLE STRUCTURE OF THE PR DOMAIN FROM PRDM16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PR DOMAIN ZINC FINGER PROTEIN 16; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PR DOMAIN (UNP RESIDUES 54-226); COMPND 5 SYNONYM: PR DOMAIN-CONTAINING PROTEIN 16, TRANSCRIPTION FACTOR MEL1, COMPND 6 MDS1/EVI1-LIKE GENE 1; COMPND 7 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: PRDM16, KIAA1675, MEL1, PFM13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST 15 KEYWDS PR DOMAIN, PRDM16, SET DOMAIN, HKMT, LYSINE METHYLTRANSFERASE, MEL1, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.SUN,G.ARMSTRONG,K.BRIKNAROVA REVDAT 1 06-JUL-16 2N1I 0 JRNL AUTH Y.SUN,G.ARMSTRONG,K.BRIKNAROVA JRNL TITL STRUCTURE OF THE PR DOMAIN FROM PRDM16 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CARTESIAN DYNAMICS AND POWELL REMARK 3 MINIMIZATION IN EXPLICIT WATER (DEFAULT ARIA REFINEMENT PROTOCOL) REMARK 4 REMARK 4 2N1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-15. REMARK 100 THE RCSB ID CODE IS RCSB104303. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.088 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.45-0.55 MM [U-99% 13C; U-99% REMARK 210 15N] PRDM16, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 2.5 MM DTT, 90% H2O/10% REMARK 210 D2O; 0.4-0.5 MM [U-99% 15N] REMARK 210 PRDM16, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 2.5 MM DTT, 90% H2O/10% REMARK 210 D2O; 0.5 MM PRDM16, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 2.5 MM DTT, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D C(CO)NH; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D HBCB(CGCD)HD; 3D 1H- REMARK 210 15N NOESY; 2D DQF-COSY; 2D 1H-1H REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ, NMRPIPE, NMRDRAW, CCPNMR, REMARK 210 ARIA, CNS, TALOS REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: 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 55 95.45 -62.12 REMARK 500 1 ASP A 59 -171.75 64.74 REMARK 500 1 PHE A 60 49.71 -97.50 REMARK 500 1 SER A 66 75.15 58.14 REMARK 500 1 ASP A 77 71.42 54.21 REMARK 500 1 ALA A 94 -71.11 -135.89 REMARK 500 1 CYS A 113 -67.67 -100.57 REMARK 500 1 PRO A 117 -165.56 -68.57 REMARK 500 1 ALA A 119 45.85 -84.88 REMARK 500 1 ALA A 121 83.79 63.20 REMARK 500 1 GLU A 123 -71.86 -57.36 REMARK 500 1 THR A 124 -60.52 -160.09 REMARK 500 1 TRP A 128 -87.16 -152.52 REMARK 500 1 GLU A 129 -47.77 175.85 REMARK 500 1 GLN A 130 94.42 -178.66 REMARK 500 1 SER A 138 80.40 51.38 REMARK 500 1 GLN A 140 32.94 -84.18 REMARK 500 1 ILE A 144 -61.82 -125.04 REMARK 500 1 THR A 145 75.43 46.62 REMARK 500 1 GLU A 154 -81.33 -86.52 REMARK 500 1 LYS A 155 47.38 -145.69 REMARK 500 1 CYS A 157 37.44 -86.09 REMARK 500 1 GLN A 162 -72.50 -118.32 REMARK 500 1 ASN A 182 38.17 -154.82 REMARK 500 1 VAL A 214 -66.89 -139.70 REMARK 500 1 TYR A 215 -56.77 -138.86 REMARK 500 1 THR A 219 -21.00 -145.63 REMARK 500 2 SER A 52 68.76 -113.13 REMARK 500 2 PRO A 55 109.64 -59.62 REMARK 500 2 PRO A 71 -159.67 -70.69 REMARK 500 2 ASP A 77 75.08 49.92 REMARK 500 2 SER A 89 127.06 -177.31 REMARK 500 2 ALA A 106 121.07 -37.42 REMARK 500 2 ARG A 118 178.99 67.30 REMARK 500 2 THR A 124 -62.18 -143.59 REMARK 500 2 TRP A 128 -78.55 -141.72 REMARK 500 2 GLU A 129 -65.13 -167.91 REMARK 500 2 LYS A 146 -62.33 -108.70 REMARK 500 2 ILE A 147 177.94 61.95 REMARK 500 2 ASP A 150 60.64 60.77 REMARK 500 2 ALA A 160 -59.13 -172.91 REMARK 500 2 ALA A 163 84.79 67.59 REMARK 500 2 ARG A 173 -166.51 -112.29 REMARK 500 2 ASN A 182 33.18 -153.90 REMARK 500 2 GLU A 212 89.45 36.25 REMARK 500 2 VAL A 214 -65.79 -108.77 REMARK 500 2 THR A 219 49.72 -85.23 REMARK 500 3 SER A 57 65.35 -153.91 REMARK 500 3 THR A 61 77.02 46.97 REMARK 500 3 PRO A 62 87.15 -68.94 REMARK 500 REMARK 500 THIS ENTRY HAS 470 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 TYR A 193 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25562 RELATED DB: BMRB DBREF 2N1I A 54 226 UNP Q9HAZ2 PRD16_HUMAN 54 226 SEQADV 2N1I GLY A 51 UNP Q9HAZ2 EXPRESSION TAG SEQADV 2N1I SER A 52 UNP Q9HAZ2 EXPRESSION TAG SEQADV 2N1I GLY A 53 UNP Q9HAZ2 EXPRESSION TAG SEQRES 1 A 176 GLY SER GLY PHE PRO THR SER GLU ASP PHE THR PRO LYS SEQRES 2 A 176 GLU GLY SER PRO TYR GLU ALA PRO VAL TYR ILE PRO GLU SEQRES 3 A 176 ASP ILE PRO ILE PRO ALA ASP PHE GLU LEU ARG GLU SER SEQRES 4 A 176 SER ILE PRO GLY ALA GLY LEU GLY VAL TRP ALA LYS ARG SEQRES 5 A 176 LYS MET GLU ALA GLY GLU ARG LEU GLY PRO CYS VAL VAL SEQRES 6 A 176 VAL PRO ARG ALA ALA ALA LYS GLU THR ASP PHE GLY TRP SEQRES 7 A 176 GLU GLN ILE LEU THR ASP VAL GLU VAL SER PRO GLN GLU SEQRES 8 A 176 GLY CYS ILE THR LYS ILE SER GLU ASP LEU GLY SER GLU SEQRES 9 A 176 LYS PHE CYS VAL ASP ALA ASN GLN ALA GLY ALA GLY SER SEQRES 10 A 176 TRP LEU LYS TYR ILE ARG VAL ALA CYS SER CYS ASP ASP SEQRES 11 A 176 GLN ASN LEU THR MET CYS GLN ILE SER GLU GLN ILE TYR SEQRES 12 A 176 TYR LYS VAL ILE LYS ASP ILE GLU PRO GLY GLU GLU LEU SEQRES 13 A 176 LEU VAL HIS VAL LYS GLU GLY VAL TYR PRO LEU GLY THR SEQRES 14 A 176 VAL PRO PRO GLY LEU ASP GLU HELIX 1 1 GLY A 166 TYR A 171 5 6 HELIX 2 2 SER A 177 GLN A 181 5 5 HELIX 3 3 TYR A 215 VAL A 220 1 6 SHEET 1 A 2 PHE A 84 ILE A 91 0 SHEET 2 A 2 GLY A 95 ALA A 100 -1 O TRP A 99 N GLU A 85 SHEET 1 B 3 ARG A 109 LEU A 110 0 SHEET 2 B 3 GLN A 191 VAL A 196 -1 O TYR A 194 N LEU A 110 SHEET 3 B 3 LEU A 183 ILE A 188 -1 N CYS A 186 O TYR A 193 CISPEP 1 GLY A 111 PRO A 112 1 -2.02 CISPEP 2 GLY A 111 PRO A 112 2 5.58 CISPEP 3 GLY A 111 PRO A 112 3 -2.56 CISPEP 4 GLY A 111 PRO A 112 4 3.17 CISPEP 5 GLY A 111 PRO A 112 5 2.33 CISPEP 6 GLY A 111 PRO A 112 6 -2.44 CISPEP 7 GLY A 111 PRO A 112 7 4.91 CISPEP 8 GLY A 111 PRO A 112 8 0.22 CISPEP 9 GLY A 111 PRO A 112 9 -2.24 CISPEP 10 GLY A 111 PRO A 112 10 -1.18 CISPEP 11 GLY A 111 PRO A 112 11 2.12 CISPEP 12 GLY A 111 PRO A 112 12 2.25 CISPEP 13 GLY A 111 PRO A 112 13 1.21 CISPEP 14 GLY A 111 PRO A 112 14 1.52 CISPEP 15 GLY A 111 PRO A 112 15 -2.14 CISPEP 16 GLY A 111 PRO A 112 16 1.08 CISPEP 17 GLY A 111 PRO A 112 17 -0.90 CISPEP 18 GLY A 111 PRO A 112 18 -0.57 CISPEP 19 GLY A 111 PRO A 112 19 -2.73 CISPEP 20 GLY A 111 PRO A 112 20 -1.55 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20