PDB Short entry for 2MJ8 HEADER PROTEIN BINDING 28-DEC-13 2MJ8 TITLE SOLUTION STRUCTURE OF CDYL2 CHROMODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMODOMAIN Y-LIKE PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-64; COMPND 5 SYNONYM: CDY-LIKE 2; COMPND 6 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: CDYL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28-MHL KEYWDS CHROMODOMAIN, PROTEIN BINDING, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.QIN,S.HOULISTON,C.H.ARROWSMITH,A.M.EDWARDS,H.WU,J.MIN,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 4 14-JUN-23 2MJ8 1 REMARK REVDAT 3 24-AUG-22 2MJ8 1 JRNL REVDAT 2 17-JUN-20 2MJ8 1 JRNL REMARK SEQADV REVDAT 1 23-APR-14 2MJ8 0 JRNL AUTH C.DONG,Y.LIU,T.J.LYU,S.BELDAR,K.N.LAMB,W.TEMPEL,Y.LI,Z.LI, JRNL AUTH 2 L.I.JAMES,S.QIN,Y.WANG,J.MIN JRNL TITL STRUCTURAL BASIS FOR THE BINDING SELECTIVITY OF HUMAN CDY JRNL TITL 2 CHROMODOMAINS. JRNL REF CELL CHEM BIOL V. 27 827 2020 JRNL REFN ESSN 2451-9456 JRNL PMID 32470319 JRNL DOI 10.1016/J.CHEMBIOL.2020.05.007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CNS REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103678. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM TRIS, 150 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D CBCA(CO)NH; REMARK 210 3D HBHA(CO)NH; 3D 1H-15N NOESY; REMARK 210 3D HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, TALOS, CYANA, REMARK 210 FMCGUI 2.5 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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 ASP A 37 96.46 -34.75 REMARK 500 1 MET A 60 67.86 60.51 REMARK 500 2 TYR A 7 -175.23 -67.74 REMARK 500 2 GLU A 8 96.93 -60.88 REMARK 500 2 ARG A 11 -177.11 173.79 REMARK 500 2 ASP A 37 110.64 -34.18 REMARK 500 3 TYR A 7 -85.61 -45.19 REMARK 500 3 ARG A 11 175.73 178.94 REMARK 500 3 ASP A 37 87.65 -11.73 REMARK 500 3 TRP A 39 79.43 -108.91 REMARK 500 4 SER A 3 82.15 59.55 REMARK 500 4 TYR A 7 -81.32 -53.97 REMARK 500 4 ASP A 37 88.92 7.46 REMARK 500 4 LEU A 46 168.44 170.27 REMARK 500 5 TYR A 7 -76.32 -53.80 REMARK 500 5 GLU A 8 78.88 -158.59 REMARK 500 5 ASP A 37 89.42 7.66 REMARK 500 5 LEU A 46 168.98 170.93 REMARK 500 5 MET A 60 -81.38 -127.05 REMARK 500 6 ASP A 5 44.09 -87.81 REMARK 500 6 TYR A 7 -75.19 -63.22 REMARK 500 6 ARG A 11 176.45 177.72 REMARK 500 6 ASP A 37 109.75 -31.80 REMARK 500 6 LEU A 46 159.85 176.89 REMARK 500 7 TYR A 7 -164.07 -63.52 REMARK 500 7 ARG A 11 179.96 175.14 REMARK 500 8 SER A 3 32.14 -160.77 REMARK 500 8 TYR A 7 -75.64 -48.98 REMARK 500 8 ARG A 11 -177.64 -178.83 REMARK 500 8 ASP A 37 111.00 -29.61 REMARK 500 8 LYS A 62 -70.46 49.18 REMARK 500 9 GLU A 8 95.93 -66.27 REMARK 500 9 ARG A 11 179.36 177.76 REMARK 500 9 ASP A 37 87.74 10.39 REMARK 500 9 LEU A 46 146.80 -176.92 REMARK 500 9 LYS A 62 119.92 69.00 REMARK 500 9 ASP A 63 45.62 -89.18 REMARK 500 10 TYR A 7 -82.45 -41.16 REMARK 500 10 ARG A 11 176.90 179.72 REMARK 500 10 TYR A 32 -62.14 -124.22 REMARK 500 10 ASP A 37 87.84 6.11 REMARK 500 11 TYR A 7 -73.50 -61.12 REMARK 500 11 ARG A 11 177.53 176.06 REMARK 500 11 ASP A 37 99.11 -10.06 REMARK 500 11 MET A 60 73.11 59.47 REMARK 500 11 SER A 61 41.45 -85.39 REMARK 500 12 ASP A 37 97.96 -26.39 REMARK 500 12 LEU A 46 144.97 -171.03 REMARK 500 13 SER A 3 23.64 -145.72 REMARK 500 13 TYR A 7 -81.86 62.08 REMARK 500 REMARK 500 THIS ENTRY HAS 81 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19710 RELATED DB: BMRB DBREF 2MJ8 A 2 64 UNP Q8N8U2 CDYL2_HUMAN 2 64 SEQADV 2MJ8 GLY A 1 UNP Q8N8U2 EXPRESSION TAG SEQRES 1 A 64 GLY ALA SER GLY ASP LEU TYR GLU VAL GLU ARG ILE VAL SEQRES 2 A 64 ASP LYS ARG LYS ASN LYS LYS GLY LYS TRP GLU TYR LEU SEQRES 3 A 64 ILE ARG TRP LYS GLY TYR GLY SER THR GLU ASP THR TRP SEQRES 4 A 64 GLU PRO GLU HIS HIS LEU LEU HIS CYS GLU GLU PHE ILE SEQRES 5 A 64 ASP GLU PHE ASN GLY LEU HIS MET SER LYS ASP LYS HELIX 1 1 TYR A 32 ASP A 37 5 6 HELIX 2 2 HIS A 43 LEU A 45 5 3 HELIX 3 3 GLU A 49 HIS A 59 1 11 SHEET 1 A 3 VAL A 9 LYS A 17 0 SHEET 2 A 3 TRP A 23 TRP A 29 -1 O GLU A 24 N ARG A 16 SHEET 3 A 3 THR A 38 PRO A 41 -1 O THR A 38 N ILE A 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