HEADER TRANSCRIPTION 23-JUN-15 5C6Q TITLE CRYSTAL STRUCTURE OF THE APO TOPLESS RELATED PROTEIN 2 (TPR2) N- TITLE 2 TERMINAL DOMAIN (1-209) FROM RICE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPR2 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 1-209); COMPND 5 SYNONYM: OS01G0254100 PROTEIN,PUTATIVE CTV.2,TOPLESS RELATED PROTEIN COMPND 6 2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 4530; SOURCE 5 GENE: P0705D01.10-1, ASPR2, OS01G0254100, OSJ_01134; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PSUMO KEYWDS TRANSCRIPTIONAL COREPRESSOR, ALPHA-HELICAL STRUCTURE, TETRAMERIC KEYWDS 2 PROTEIN, PLANT TRANSCRIPTIONAL REPRESSION, TRANSCRIPTION, PLANT KEYWDS 3 DEVELOPMENT EXPDTA X-RAY DIFFRACTION AUTHOR J.KE,H.MA,X.GU,J.S.BRUNZELLE,H.E.XU,K.MELCHER REVDAT 5 27-SEP-23 5C6Q 1 REMARK REVDAT 4 25-DEC-19 5C6Q 1 REMARK REVDAT 3 27-SEP-17 5C6Q 1 REMARK REVDAT 2 09-DEC-15 5C6Q 1 JRNL REVDAT 1 05-AUG-15 5C6Q 0 JRNL AUTH J.KE,H.MA,X.GU,A.THELEN,J.S.BRUNZELLE,J.LI,H.E.XU,K.MELCHER JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF DIVERSE TRANSCRIPTIONAL JRNL TITL 2 REPRESSORS BY THE TOPLESS FAMILY OF COREPRESSORS. JRNL REF SCI ADV V. 1 00107 2015 JRNL REFN ESSN 2375-2548 JRNL PMID 26601214 JRNL DOI 10.1126/SCIADV.1500107 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.570 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9103 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.530 REMARK 3 FREE R VALUE TEST SET COUNT : 412 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 34.7123 - 4.6857 1.00 2899 137 0.1944 0.2728 REMARK 3 2 4.6857 - 3.7205 1.00 2891 143 0.2182 0.2473 REMARK 3 3 3.7205 - 3.2506 1.00 2901 132 0.2891 0.3153 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.180 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 : 0.008 1738 REMARK 3 ANGLE : 1.281 2337 REMARK 3 CHIRALITY : 0.050 258 REMARK 3 PLANARITY : 0.008 296 REMARK 3 DIHEDRAL : 16.489 659 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 5C6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000211093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.27821 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10544 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4ZHE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2 M MAGNESIUM REMARK 280 CHLORIDE, 0.1 M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.48550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.48550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.87150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.48550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.48550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 85.87150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.48550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.48550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.87150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.48550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.48550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 85.87150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 PRO A 206 REMARK 465 PRO A 207 REMARK 465 ASN A 208 REMARK 465 GLY A 209 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 158 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 ASN A 188 CG OD1 ND2 REMARK 470 ASN A 192 CG OD1 ND2 REMARK 470 ASP A 194 CG OD1 OD2 REMARK 470 LYS A 196 CG CD CE NZ REMARK 470 THR A 205 OG1 CG2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 183 ND1 REMARK 620 2 CYS A 186 SG 146.3 REMARK 620 3 HIS A 202 NE2 107.7 92.4 REMARK 620 4 CYS A 204 SG 102.3 100.7 99.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZHE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SEMET SUBSTITUTED TOPLESS RELATED PROTEIN REMARK 900 2 (TPR2) N-TERMINAL DOMAIN (1-209) FROM RICE. REMARK 900 RELATED ID: 5C7E RELATED DB: PDB REMARK 900 RELATED ID: 5C6V RELATED DB: PDB REMARK 900 RELATED ID: 5C7F RELATED DB: PDB DBREF 5C6Q A 1 209 UNP Q5NBT9 Q5NBT9_ORYSJ 1 209 SEQRES 1 A 209 MET SER SER LEU SER ARG GLU LEU VAL PHE LEU ILE LEU SEQRES 2 A 209 GLN PHE LEU ASP GLU GLU LYS PHE LYS GLU THR VAL HIS SEQRES 3 A 209 LYS LEU GLU GLN GLU SER GLY PHE PHE PHE ASN MET LYS SEQRES 4 A 209 TYR PHE GLU GLU LYS VAL HIS ALA GLY GLU TRP ASP GLU SEQRES 5 A 209 VAL GLU LYS TYR LEU SER GLY PHE THR LYS VAL ASP ASP SEQRES 6 A 209 ASN ARG TYR SER MET LYS ILE PHE PHE GLU ILE ARG LYS SEQRES 7 A 209 GLN LYS TYR LEU GLU ALA LEU ASP ARG HIS ASP ARG ALA SEQRES 8 A 209 LYS ALA VAL ASP ILE LEU VAL LYS ASP LEU LYS VAL PHE SEQRES 9 A 209 SER THR PHE ASN GLU GLU LEU TYR LYS GLU ILE THR GLN SEQRES 10 A 209 LEU LEU THR LEU GLU ASN PHE ARG GLU ASN GLU GLN LEU SEQRES 11 A 209 SER LYS TYR GLY ASP THR LYS SER ALA ARG SER ILE MET SEQRES 12 A 209 LEU ILE GLU LEU LYS LYS LEU ILE GLU ALA ASN PRO LEU SEQRES 13 A 209 PHE ARG GLU LYS LEU VAL PHE PRO THR LEU LYS ALA SER SEQRES 14 A 209 ARG LEU ARG THR LEU ILE ASN GLN SER LEU ASN TRP GLN SEQRES 15 A 209 HIS GLN LEU CYS LYS ASN PRO ARG PRO ASN PRO ASP ILE SEQRES 16 A 209 LYS THR LEU PHE THR ASP HIS THR CYS THR PRO PRO ASN SEQRES 17 A 209 GLY HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *4(H2 O) HELIX 1 AA1 SER A 2 GLU A 19 1 18 HELIX 2 AA2 PHE A 21 GLY A 33 1 13 HELIX 3 AA3 ASN A 37 ALA A 47 1 11 HELIX 4 AA4 GLU A 49 SER A 58 1 10 HELIX 5 AA5 ASN A 66 ARG A 87 1 22 HELIX 6 AA6 ASP A 89 ASP A 100 1 12 HELIX 7 AA7 LEU A 101 SER A 105 5 5 HELIX 8 AA8 ASN A 108 GLN A 117 1 10 HELIX 9 AA9 LEU A 118 LEU A 121 5 4 HELIX 10 AB1 ASN A 123 ASN A 127 5 5 HELIX 11 AB2 ASP A 135 ASN A 154 1 20 HELIX 12 AB3 SER A 169 GLN A 184 1 16 LINK ND1 HIS A 183 ZN ZN A 401 1555 1555 1.93 LINK SG CYS A 186 ZN ZN A 401 1555 1555 2.14 LINK NE2 HIS A 202 ZN ZN A 401 1555 1555 2.19 LINK SG CYS A 204 ZN ZN A 401 1555 1555 2.29 CISPEP 1 LYS A 187 ASN A 188 0 -2.63 SITE 1 AC1 4 HIS A 183 CYS A 186 HIS A 202 CYS A 204 CRYST1 58.971 58.971 171.743 90.00 90.00 90.00 P 42 21 2 8 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 0.016957 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005823 0.00000