HEADER SIGNALING PROTEIN 19-APR-07 2YW5 TITLE SOLUTION STRUCTURE OF THE BROMODOMAIN FROM HUMAN BROMODOMAIN TITLE 2 CONTAINING PROTEIN 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-155, BROMODOMAIN; COMPND 5 SYNONYM: RING3-LIKE PROTEIN; 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: BRD3, KIAA0043, RING3L; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P060731-10; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS BROMODOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.FURUE,S.SUZUKI,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 29-MAY-24 2YW5 1 REMARK REVDAT 3 16-MAR-22 2YW5 1 REMARK SEQADV REVDAT 2 24-FEB-09 2YW5 1 VERSN REVDAT 1 22-APR-08 2YW5 0 JRNL AUTH M.FURUE,S.SUZUKI,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA, JRNL AUTH 2 M.SHIROUZU,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE BROMODOMAIN FROM HUMAN BROMODOMAIN JRNL TITL 2 CONTAINING PROTEIN 3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 9 REMARK 3 AUTHORS : BRUKER (XWINNMR), CASE, D.A. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YW5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000027209. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2MM 13C/15N-PROTEIN; 20MM D REMARK 210 -TRIS-HCL(PH7.0); 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_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 20060702, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9825, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYANAMICS, REMARK 210 SIMULATED ANNEALING, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY,TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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: 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 89 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 19 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.1 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 GLU A 91 1.92 -67.73 REMARK 500 2 SER A 20 48.33 -71.67 REMARK 500 2 VAL A 45 -50.13 -130.64 REMARK 500 2 TYR A 94 -40.71 -140.53 REMARK 500 3 VAL A 45 -50.18 -136.99 REMARK 500 3 ASN A 93 65.75 37.24 REMARK 500 4 SER A 19 39.24 -74.51 REMARK 500 4 VAL A 45 -54.65 -127.53 REMARK 500 4 TYR A 94 -38.12 -148.25 REMARK 500 5 SER A 19 68.48 -151.19 REMARK 500 5 SER A 30 -24.92 -141.82 REMARK 500 5 VAL A 45 -53.56 -130.28 REMARK 500 5 ASN A 79 81.63 -153.16 REMARK 500 5 GLU A 91 3.61 -68.18 REMARK 500 5 ASN A 93 37.50 -83.31 REMARK 500 6 VAL A 45 -41.08 -138.83 REMARK 500 7 VAL A 45 -49.67 -133.60 REMARK 500 7 LEU A 70 78.96 -116.10 REMARK 500 7 TYR A 94 -34.48 -155.54 REMARK 500 8 VAL A 45 -52.18 -128.40 REMARK 500 8 LEU A 70 78.24 -113.92 REMARK 500 8 ASN A 93 34.20 -99.12 REMARK 500 9 SER A 19 -3.74 63.99 REMARK 500 9 VAL A 45 -48.61 -131.84 REMARK 500 9 ASN A 93 36.89 -78.34 REMARK 500 10 SER A 30 -32.63 -156.48 REMARK 500 10 VAL A 45 -51.40 -129.20 REMARK 500 10 PRO A 152 36.94 -77.38 REMARK 500 11 SER A 19 36.92 -145.91 REMARK 500 11 VAL A 26 -27.57 -148.46 REMARK 500 11 VAL A 45 -50.66 -133.85 REMARK 500 11 ASN A 93 56.72 34.86 REMARK 500 12 VAL A 45 -51.68 -127.96 REMARK 500 12 TYR A 94 -33.77 -137.09 REMARK 500 13 VAL A 45 -49.83 -130.38 REMARK 500 13 ASP A 64 78.77 -69.57 REMARK 500 13 ASN A 93 42.54 -105.39 REMARK 500 14 VAL A 45 -50.26 -132.81 REMARK 500 14 TYR A 94 -37.78 -131.24 REMARK 500 15 VAL A 45 -50.26 -134.07 REMARK 500 16 VAL A 45 -48.55 -133.64 REMARK 500 17 SER A 22 108.64 -54.77 REMARK 500 17 VAL A 26 -7.27 -141.24 REMARK 500 17 SER A 27 29.26 -142.88 REMARK 500 17 PRO A 29 -167.61 -79.71 REMARK 500 17 SER A 30 29.29 49.29 REMARK 500 17 VAL A 45 -48.45 -135.89 REMARK 500 17 ASP A 64 85.81 -69.87 REMARK 500 17 ASN A 93 37.00 -75.94 REMARK 500 18 VAL A 45 -53.08 -133.03 REMARK 500 REMARK 500 THIS ENTRY HAS 57 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 19 TYR A 94 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002100040.2 RELATED DB: TARGETDB DBREF 2YW5 A 25 155 UNP Q15059 BRD3_HUMAN 25 155 SEQADV 2YW5 GLY A 18 UNP Q15059 EXPRESSION TAG SEQADV 2YW5 SER A 19 UNP Q15059 EXPRESSION TAG SEQADV 2YW5 SER A 20 UNP Q15059 EXPRESSION TAG SEQADV 2YW5 GLY A 21 UNP Q15059 EXPRESSION TAG SEQADV 2YW5 SER A 22 UNP Q15059 EXPRESSION TAG SEQADV 2YW5 SER A 23 UNP Q15059 EXPRESSION TAG SEQADV 2YW5 GLY A 24 UNP Q15059 EXPRESSION TAG SEQRES 1 A 138 GLY SER SER GLY SER SER GLY GLU VAL SER ASN PRO SER SEQRES 2 A 138 LYS PRO GLY ARG LYS THR ASN GLN LEU GLN TYR MET GLN SEQRES 3 A 138 ASN VAL VAL VAL LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 A 138 TRP PRO PHE TYR GLN PRO VAL ASP ALA ILE LYS LEU ASN SEQRES 5 A 138 LEU PRO ASP TYR HIS LYS ILE ILE LYS ASN PRO MET ASP SEQRES 6 A 138 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 138 TRP SER ALA SER GLU CYS MET GLN ASP PHE ASN THR MET SEQRES 8 A 138 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP SEQRES 9 A 138 ILE VAL LEU MET ALA GLN ALA LEU GLU LYS ILE PHE LEU SEQRES 10 A 138 GLN LYS VAL ALA GLN MET PRO GLN GLU GLU VAL GLU LEU SEQRES 11 A 138 LEU PRO PRO ALA PRO LYS GLY LYS HELIX 1 1 THR A 36 VAL A 45 1 10 HELIX 2 2 VAL A 45 HIS A 53 1 9 HELIX 3 3 ALA A 56 TYR A 60 5 5 HELIX 4 4 ASP A 72 ILE A 77 1 6 HELIX 5 5 ASP A 82 GLU A 91 1 10 HELIX 6 6 SER A 97 ASN A 116 1 20 HELIX 7 7 ASP A 120 MET A 140 1 21 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