HEADER HYDROLASE 07-SEP-06 2DY8 TITLE SOLUTION STRUCTURE OF THE SECOND CHROMODOMAIN OF YEAST CHD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMO DOMAIN PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CHROMODOMAIN 2; COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE CHD1; COMPND 6 EC: 3.6.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: CHD1/YER164W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS CHROMATIN REMODELING, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.OKUDA,Y.NISHIMURA REVDAT 4 09-MAR-22 2DY8 1 REMARK REVDAT 3 24-FEB-09 2DY8 1 VERSN REVDAT 2 16-JAN-07 2DY8 1 JRNL REVDAT 1 28-NOV-06 2DY8 0 JRNL AUTH M.OKUDA,M.HORIKOSHI,Y.NISHIMURA JRNL TITL STRUCTURAL POLYMORPHISM OF CHROMODOMAINS IN CHD1 JRNL REF J.MOL.BIOL. V. 365 1047 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17098252 JRNL DOI 10.1016/J.JMB.2006.10.039 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, X-PLOR REMARK 3 AUTHORS : BRUNGER, A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DY8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000025991. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 300MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3-0.5MM CHROMODOMAIN; 20MM REMARK 210 POTASSIUM PHOSPHATE BUFFER; 90% REMARK 210 H2O, 10% D2O; 0.3-0.5MM REMARK 210 CHROMODOMAIN; 20MM POTASSIUM REMARK 210 PHOSPHATE BUFFER; 100% D2O; 0.3- REMARK 210 0.5MM CHROMODOMAIN U-15N; 20MM REMARK 210 POTASSIUM PHOSPHATE BUFFER; 90% REMARK 210 H2O, 10% D2O; 0.3-0.5MM REMARK 210 CHROMODOMAIN U-13C,15N; 20MM REMARK 210 POTASSIUM PHOSPHATE BUFFER; 90% REMARK 210 H2O, 10% D2O; 0.3-0.5MM REMARK 210 CHROMODOMAIN U-13C,15N; 20MM REMARK 210 POTASSIUM PHOSPHATE BUFFER; 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; HNHA; HNHB; REMARK 210 HN(CO)HB; HNCG; HN(CO)CG REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 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: 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 O ALA A 296 H GLN A 304 1.52 REMARK 500 O ASP A 326 H LEU A 330 1.53 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 PHE A 281 67.86 -101.07 REMARK 500 1 GLU A 283 -81.12 -131.75 REMARK 500 1 GLU A 299 -11.39 76.83 REMARK 500 1 THR A 302 -161.35 -161.29 REMARK 500 1 ARG A 312 -165.46 55.05 REMARK 500 1 LEU A 314 155.38 57.77 REMARK 500 1 TYR A 316 -87.07 -100.51 REMARK 500 1 GLU A 318 121.79 -176.92 REMARK 500 1 THR A 320 -159.43 -140.49 REMARK 500 1 ILE A 346 93.60 43.99 REMARK 500 2 GLU A 283 59.19 -114.28 REMARK 500 2 LEU A 298 -82.94 -85.93 REMARK 500 2 GLU A 299 -35.97 174.66 REMARK 500 2 ARG A 313 -93.13 41.14 REMARK 500 2 LEU A 314 24.97 -162.07 REMARK 500 2 ASP A 317 117.95 -177.98 REMARK 500 2 GLU A 318 65.65 -177.70 REMARK 500 2 SER A 344 50.98 -168.13 REMARK 500 3 GLU A 280 88.31 -61.89 REMARK 500 3 GLU A 299 -16.03 79.09 REMARK 500 3 THR A 302 -158.32 -162.48 REMARK 500 3 ARG A 312 77.48 -62.85 REMARK 500 3 ASN A 315 -163.71 179.37 REMARK 500 3 ASP A 317 153.65 63.64 REMARK 500 3 ALA A 319 137.10 64.58 REMARK 500 3 THR A 320 -160.19 -128.55 REMARK 500 3 SER A 344 101.94 -167.35 REMARK 500 4 PHE A 281 56.28 -176.85 REMARK 500 4 GLU A 282 -81.39 -44.61 REMARK 500 4 PHE A 284 -65.19 -154.43 REMARK 500 4 ARG A 289 169.40 175.82 REMARK 500 4 GLU A 299 -18.92 78.88 REMARK 500 4 THR A 302 -168.35 -162.76 REMARK 500 4 ARG A 312 56.73 -90.17 REMARK 500 4 TYR A 316 -158.57 46.39 REMARK 500 4 GLU A 318 -158.19 -172.53 REMARK 500 4 ASN A 343 71.97 -171.59 REMARK 500 4 SER A 344 28.64 -161.06 REMARK 500 4 LYS A 345 117.28 178.80 REMARK 500 5 GLU A 280 76.00 -65.14 REMARK 500 5 GLU A 282 -91.58 46.63 REMARK 500 5 GLU A 283 17.10 56.90 REMARK 500 5 GLU A 299 -20.95 80.37 REMARK 500 5 THR A 302 -162.24 -161.77 REMARK 500 5 ASN A 315 -60.08 -141.05 REMARK 500 5 ASP A 317 125.55 -176.29 REMARK 500 5 ALA A 319 147.21 61.02 REMARK 500 5 THR A 320 -158.73 -151.77 REMARK 500 5 ASN A 343 92.94 -176.69 REMARK 500 5 SER A 344 148.34 176.30 REMARK 500 REMARK 500 THIS ENTRY HAS 207 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 1 ARG A 289 0.23 SIDE CHAIN REMARK 500 1 ARG A 295 0.28 SIDE CHAIN REMARK 500 1 ARG A 312 0.16 SIDE CHAIN REMARK 500 1 ARG A 313 0.16 SIDE CHAIN REMARK 500 1 ARG A 341 0.14 SIDE CHAIN REMARK 500 2 ARG A 289 0.23 SIDE CHAIN REMARK 500 2 ARG A 295 0.26 SIDE CHAIN REMARK 500 2 ARG A 312 0.16 SIDE CHAIN REMARK 500 2 ARG A 313 0.28 SIDE CHAIN REMARK 500 2 ARG A 341 0.29 SIDE CHAIN REMARK 500 3 ARG A 289 0.25 SIDE CHAIN REMARK 500 3 ARG A 295 0.24 SIDE CHAIN REMARK 500 3 ARG A 312 0.23 SIDE CHAIN REMARK 500 3 ARG A 313 0.30 SIDE CHAIN REMARK 500 3 ARG A 341 0.29 SIDE CHAIN REMARK 500 4 ARG A 289 0.30 SIDE CHAIN REMARK 500 4 ARG A 295 0.18 SIDE CHAIN REMARK 500 4 ARG A 312 0.29 SIDE CHAIN REMARK 500 4 ARG A 313 0.32 SIDE CHAIN REMARK 500 4 ARG A 341 0.29 SIDE CHAIN REMARK 500 5 ARG A 289 0.32 SIDE CHAIN REMARK 500 5 ARG A 295 0.14 SIDE CHAIN REMARK 500 5 ARG A 312 0.18 SIDE CHAIN REMARK 500 5 ARG A 313 0.27 SIDE CHAIN REMARK 500 5 ARG A 341 0.32 SIDE CHAIN REMARK 500 6 ARG A 289 0.14 SIDE CHAIN REMARK 500 6 ARG A 295 0.22 SIDE CHAIN REMARK 500 6 ARG A 312 0.12 SIDE CHAIN REMARK 500 6 ARG A 313 0.21 SIDE CHAIN REMARK 500 6 ARG A 341 0.18 SIDE CHAIN REMARK 500 7 ARG A 289 0.30 SIDE CHAIN REMARK 500 7 ARG A 295 0.21 SIDE CHAIN REMARK 500 7 ARG A 312 0.18 SIDE CHAIN REMARK 500 7 ARG A 313 0.31 SIDE CHAIN REMARK 500 7 ARG A 341 0.32 SIDE CHAIN REMARK 500 8 ARG A 289 0.26 SIDE CHAIN REMARK 500 8 ARG A 295 0.15 SIDE CHAIN REMARK 500 8 ARG A 312 0.21 SIDE CHAIN REMARK 500 8 ARG A 313 0.23 SIDE CHAIN REMARK 500 8 ARG A 341 0.14 SIDE CHAIN REMARK 500 9 ARG A 289 0.32 SIDE CHAIN REMARK 500 9 ARG A 295 0.32 SIDE CHAIN REMARK 500 9 ARG A 312 0.31 SIDE CHAIN REMARK 500 9 ARG A 313 0.22 SIDE CHAIN REMARK 500 9 ARG A 341 0.32 SIDE CHAIN REMARK 500 10 ARG A 289 0.29 SIDE CHAIN REMARK 500 10 ARG A 295 0.29 SIDE CHAIN REMARK 500 10 ARG A 312 0.28 SIDE CHAIN REMARK 500 10 ARG A 313 0.32 SIDE CHAIN REMARK 500 10 ARG A 341 0.17 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 98 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DY7 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE FIRST CHROMODOMAIN OF YEAST CHD1 DBREF 2DY8 A 279 347 UNP P32657 CHD1_YEAST 279 347 SEQRES 1 A 69 ASP GLU PHE GLU GLU PHE HIS VAL PRO GLU ARG ILE ILE SEQRES 2 A 69 ASP SER GLN ARG ALA SER LEU GLU ASP GLY THR SER GLN SEQRES 3 A 69 LEU GLN TYR LEU VAL LYS TRP ARG ARG LEU ASN TYR ASP SEQRES 4 A 69 GLU ALA THR TRP GLU ASN ALA THR ASP ILE VAL LYS LEU SEQRES 5 A 69 ALA PRO GLU GLN VAL LYS HIS PHE GLN ASN ARG GLU ASN SEQRES 6 A 69 SER LYS ILE LEU HELIX 1 1 ALA A 324 ALA A 331 1 8 HELIX 2 2 GLU A 333 GLU A 342 1 10 SHEET 1 A 3 PRO A 287 GLU A 299 0 SHEET 2 A 3 THR A 302 TRP A 311 -1 O GLN A 304 N ALA A 296 SHEET 3 A 3 THR A 320 ASN A 323 -1 O GLU A 322 N TYR A 307 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