HEADER TRANSCRIPTION 07-MAR-16 5IN1 TITLE CRYSTAL STRUCTURE OF THE MRG701 CHROMODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MRG701; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CHROMODOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 4530; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS MRG701, CHROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.HUANG,Y.LIU REVDAT 2 08-NOV-23 5IN1 1 REMARK REVDAT 1 01-MAR-17 5IN1 0 JRNL AUTH Y.LIU,H.WU,Y.YU,Y.HUANG JRNL TITL STRUCTURAL STUDIES ON MRG701 CHROMODOMAIN REVEAL A NOVEL JRNL TITL 2 DIMERIZATION INTERFACE OF MRG PROTEINS IN GREEN PLANTS JRNL REF PROTEIN CELL V. 7 792 2016 JRNL REFN ESSN 1674-8018 JRNL PMID 27638467 JRNL DOI 10.1007/S13238-016-0310-5 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 28840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.9073 - 3.3722 0.97 1941 144 0.1705 0.1906 REMARK 3 2 3.3722 - 2.6771 0.99 1928 143 0.1906 0.1944 REMARK 3 3 2.6771 - 2.3389 0.98 1919 143 0.1939 0.2136 REMARK 3 4 2.3389 - 2.1251 0.99 1920 143 0.1807 0.2012 REMARK 3 5 2.1251 - 1.9728 0.99 1928 144 0.1737 0.2091 REMARK 3 6 1.9728 - 1.8565 0.98 1898 141 0.1829 0.2153 REMARK 3 7 1.8565 - 1.7636 0.98 1902 142 0.1824 0.2024 REMARK 3 8 1.7636 - 1.6868 0.99 1925 143 0.1861 0.2104 REMARK 3 9 1.6868 - 1.6219 0.99 1938 145 0.1867 0.2039 REMARK 3 10 1.6219 - 1.5659 0.98 1893 141 0.1819 0.2146 REMARK 3 11 1.5659 - 1.5169 0.99 1912 142 0.1769 0.2165 REMARK 3 12 1.5169 - 1.4736 0.99 1920 144 0.1839 0.2042 REMARK 3 13 1.4736 - 1.4348 0.99 1907 142 0.1907 0.2204 REMARK 3 14 1.4348 - 1.3998 0.98 1910 142 0.1877 0.2286 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1278 REMARK 3 ANGLE : 1.049 1718 REMARK 3 CHIRALITY : 0.046 166 REMARK 3 PLANARITY : 0.005 216 REMARK 3 DIHEDRAL : 14.869 478 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5IN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28872 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4PLI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH 4.5, 25% PEG REMARK 280 4000, 0.2M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.90050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 9 REMARK 465 GLY B 9 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HOH A 173 O HOH A 203 1.89 REMARK 500 O HOH A 129 O HOH A 186 1.92 REMARK 500 NZ LYS B 29 O HOH B 201 1.94 REMARK 500 O LEU B 25 O HOH B 202 1.98 REMARK 500 O HOH B 252 O HOH B 266 2.01 REMARK 500 O HOH B 291 O HOH B 325 2.02 REMARK 500 NZ LYS A 29 O HOH A 101 2.02 REMARK 500 O HOH B 233 O HOH B 314 2.04 REMARK 500 NZ LYS A 29 O HOH A 102 2.07 REMARK 500 OE1 GLU A 75 O HOH A 103 2.08 REMARK 500 OG SER B 50 O HOH B 203 2.08 REMARK 500 NZ LYS B 51 O HOH B 204 2.11 REMARK 500 O HOH B 292 O HOH B 304 2.12 REMARK 500 O HOH A 108 O HOH A 140 2.12 REMARK 500 O HOH B 287 O HOH B 304 2.15 REMARK 500 OE1 GLU A 37 O HOH A 104 2.16 REMARK 500 O4 SO4 B 102 O HOH B 205 2.16 REMARK 500 O3 SO4 B 101 O HOH B 206 2.18 REMARK 500 O HOH A 205 O HOH A 207 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 160 O HOH B 321 1556 1.92 REMARK 500 O HOH A 153 O HOH B 309 1556 1.99 REMARK 500 O HOH A 110 O HOH B 321 1556 2.04 REMARK 500 O HOH A 106 O HOH B 284 1456 2.13 REMARK 500 O HOH A 123 O HOH B 211 2645 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PLI RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHROMODOMAIN OF MRG2 IN COMPLEX WITH H3K36ME3 DBREF 5IN1 A 9 80 PDB 5IN1 5IN1 9 80 DBREF 5IN1 B 9 80 PDB 5IN1 5IN1 9 80 SEQRES 1 A 72 GLY SER PHE LYS GLU GLY GLU ARG VAL LEU ALA TYR HIS SEQRES 2 A 72 GLY PRO LEU LEU TYR GLU ALA LYS VAL GLN LYS SER GLU SEQRES 3 A 72 ASN LYS GLU ASP GLU TRP ARG TYR HIS VAL HIS TYR LEU SEQRES 4 A 72 GLY TRP SER LYS SER TRP ASP GLU TRP VAL THR ASN ASP SEQRES 5 A 72 ARG LEU LEU LYS LEU THR ASP GLU ASN ILE ARG LYS GLN SEQRES 6 A 72 GLN GLU LEU GLU LYS SER GLN SEQRES 1 B 72 GLY SER PHE LYS GLU GLY GLU ARG VAL LEU ALA TYR HIS SEQRES 2 B 72 GLY PRO LEU LEU TYR GLU ALA LYS VAL GLN LYS SER GLU SEQRES 3 B 72 ASN LYS GLU ASP GLU TRP ARG TYR HIS VAL HIS TYR LEU SEQRES 4 B 72 GLY TRP SER LYS SER TRP ASP GLU TRP VAL THR ASN ASP SEQRES 5 B 72 ARG LEU LEU LYS LEU THR ASP GLU ASN ILE ARG LYS GLN SEQRES 6 B 72 GLN GLU LEU GLU LYS SER GLN HET SO4 B 101 5 HET SO4 B 102 5 HET EDO B 103 4 HET EDO B 104 4 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 EDO 2(C2 H6 O2) FORMUL 7 HOH *252(H2 O) HELIX 1 AA1 SER A 50 ASP A 54 5 5 HELIX 2 AA2 THR A 66 SER A 79 1 14 HELIX 3 AA3 SER B 50 ASP B 54 5 5 HELIX 4 AA4 THR B 58 ASP B 60 5 3 HELIX 5 AA5 THR B 66 SER B 79 1 14 SHEET 1 AA1 6 GLU A 55 THR A 58 0 SHEET 2 AA1 6 GLU A 39 TYR A 46 -1 N VAL A 44 O GLU A 55 SHEET 3 AA1 6 LEU A 24 LYS A 36 -1 N GLN A 31 O HIS A 43 SHEET 4 AA1 6 LEU B 24 LYS B 36 -1 O ASN B 35 N ASN A 35 SHEET 5 AA1 6 GLU B 39 TYR B 46 -1 O HIS B 43 N GLN B 31 SHEET 6 AA1 6 GLU B 55 VAL B 57 -1 O GLU B 55 N VAL B 44 SHEET 1 AA2 6 LEU A 62 LYS A 64 0 SHEET 2 AA2 6 ARG A 16 HIS A 21 -1 N LEU A 18 O LEU A 63 SHEET 3 AA2 6 LEU A 24 LYS A 36 -1 O TYR A 26 N ALA A 19 SHEET 4 AA2 6 LEU B 24 LYS B 36 -1 O ASN B 35 N ASN A 35 SHEET 5 AA2 6 ARG B 16 HIS B 21 -1 N VAL B 17 O ALA B 28 SHEET 6 AA2 6 LEU B 62 LYS B 64 -1 O LEU B 63 N LEU B 18 SITE 1 AC1 6 THR B 66 ASP B 67 HOH B 206 HOH B 212 SITE 2 AC1 6 HOH B 225 HOH B 235 SITE 1 AC2 9 SER B 50 LYS B 51 HOH B 203 HOH B 205 SITE 2 AC2 9 HOH B 247 HOH B 261 HOH B 262 HOH B 265 SITE 3 AC2 9 HOH B 271 SITE 1 AC3 7 TYR A 26 GLU A 27 LEU B 25 GLU B 77 SITE 2 AC3 7 HOH B 202 HOH B 239 HOH B 253 SITE 1 AC4 6 LEU A 25 GLU A 77 TYR B 26 GLU B 27 SITE 2 AC4 6 HOH B 251 HOH B 254 CRYST1 31.786 59.801 40.616 90.00 102.58 90.00 P 1 21 1 4 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 0.031460 0.000000 0.007022 0.00000 SCALE2 0.000000 0.016722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025227 0.00000