HEADER DNA BINDING PROTEIN 12-MAY-21 7ET5 TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS TEM1 AP2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP2/ERF AND B3 DOMAIN-CONTAINING TRANSCRIPTION REPRESSOR COMPND 3 TEM1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: AP2 DOMAIN; COMPND 6 SYNONYM: PROTEIN TEMPRANILLO 1,RAV1-LIKE ETHYLENE-RESPONSIVE COMPND 7 TRANSCRIPTION FACTOR TEM1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: TEM1, AT1G25560, F2J7.3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DE3; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS GENE REGULATION, FLOWERING TIME REGULATION, PLANT PROTEIN, DNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.HU,J.DU REVDAT 2 29-NOV-23 7ET5 1 REMARK REVDAT 1 15-SEP-21 7ET5 0 JRNL AUTH H.HU,S.TIAN,G.XIE,R.LIU,N.WANG,S.LI,Y.HE,J.DU JRNL TITL TEM1 COMBINATORIALLY BINDS TO FLOWERING LOCUS T AND RECRUITS JRNL TITL 2 A POLYCOMB FACTOR TO REPRESS THE FLORAL TRANSITION IN JRNL TITL 3 ARABIDOPSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34446554 JRNL DOI 10.1073/PNAS.2103895118 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 42669 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2078 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 10.0000 - 2.5944 1.00 2990 147 0.0000 0.1819 REMARK 3 2 2.5944 - 2.0593 1.00 2846 148 0.1627 0.1672 REMARK 3 3 2.0593 - 1.7990 1.00 2794 156 0.1509 0.1701 REMARK 3 4 1.7990 - 1.6345 0.99 2776 145 0.1444 0.1534 REMARK 3 5 1.6345 - 1.5174 0.99 2753 145 0.1361 0.1475 REMARK 3 6 1.5174 - 1.4279 0.98 2729 136 0.1354 0.1765 REMARK 3 7 1.4279 - 1.3564 0.98 2709 149 0.1385 0.1735 REMARK 3 8 1.3564 - 1.2974 0.98 2678 142 0.1370 0.1596 REMARK 3 9 1.2974 - 1.2474 0.97 2701 125 0.1351 0.1598 REMARK 3 10 1.2474 - 1.2044 0.97 2650 153 0.1495 0.1554 REMARK 3 11 1.2044 - 1.1667 0.96 2651 158 0.1655 0.2063 REMARK 3 12 1.1667 - 1.1333 0.95 2618 115 0.1806 0.2313 REMARK 3 13 1.1333 - 1.1035 0.96 2643 122 0.1818 0.2131 REMARK 3 14 1.1035 - 1.0766 0.94 2592 135 0.2110 0.2311 REMARK 3 15 1.0766 - 1.0521 0.88 2461 102 0.0000 0.2285 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.16 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7ET5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300020552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42719 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 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 (%) : 96.2 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.79100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: 1GCC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LI2SO4, 0.1 M TRIS PH 8.5, 18% REMARK 280 PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 18.82500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.98300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.98300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.82500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.60000 REMARK 290 SMTRY3 4 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: 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 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 SER A 49 REMARK 465 SER A 50 REMARK 465 SER A 51 REMARK 465 VAL A 52 REMARK 465 VAL A 53 REMARK 465 LEU A 54 REMARK 465 ASP A 55 REMARK 465 SER A 56 REMARK 465 GLU A 57 REMARK 465 ASN A 58 REMARK 465 GLY A 59 REMARK 465 VAL A 60 REMARK 465 GLU A 61 REMARK 465 THR A 62 REMARK 465 GLU A 63 REMARK 465 SER A 64 REMARK 465 ARG A 65 REMARK 465 LYS A 66 REMARK 465 LEU A 67 REMARK 465 PRO A 68 REMARK 465 VAL A 168 REMARK 465 ASN A 169 REMARK 465 GLY A 170 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 DBREF 7ET5 A 50 170 UNP Q9C6M5 RAVL1_ARATH 50 170 SEQADV 7ET5 SER A 49 UNP Q9C6M5 EXPRESSION TAG SEQRES 1 A 122 SER SER SER VAL VAL LEU ASP SER GLU ASN GLY VAL GLU SEQRES 2 A 122 THR GLU SER ARG LYS LEU PRO SER SER LYS TYR LYS GLY SEQRES 3 A 122 VAL VAL PRO GLN PRO ASN GLY ARG TRP GLY ALA GLN ILE SEQRES 4 A 122 TYR GLU LYS HIS GLN ARG VAL TRP LEU GLY THR PHE ASN SEQRES 5 A 122 GLU GLU GLU GLU ALA ALA SER SER TYR ASP ILE ALA VAL SEQRES 6 A 122 ARG ARG PHE ARG GLY ARG ASP ALA VAL THR ASN PHE LYS SEQRES 7 A 122 SER GLN VAL ASP GLY ASN ASP ALA GLU SER ALA PHE LEU SEQRES 8 A 122 ASP ALA HIS SER LYS ALA GLU ILE VAL ASP MET LEU ARG SEQRES 9 A 122 LYS HIS THR TYR ALA ASP GLU PHE GLU GLN SER ARG ARG SEQRES 10 A 122 LYS PHE VAL ASN GLY HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *120(H2 O) HELIX 1 AA1 GLU A 101 GLY A 118 1 18 HELIX 2 AA2 ARG A 119 ALA A 121 5 3 HELIX 3 AA3 ASP A 133 ALA A 141 1 9 HELIX 4 AA4 SER A 143 LYS A 153 1 11 HELIX 5 AA5 THR A 155 ARG A 164 1 10 SHEET 1 AA1 3 VAL A 75 PRO A 77 0 SHEET 2 AA1 3 TRP A 83 GLU A 89 -1 O GLY A 84 N VAL A 76 SHEET 3 AA1 3 GLN A 92 PHE A 99 -1 O PHE A 99 N TRP A 83 SITE 1 AC1 11 TRP A 95 GLY A 97 THR A 98 ARG A 115 SITE 2 AC1 11 SER A 143 LYS A 144 HOH A 314 HOH A 333 SITE 3 AC1 11 HOH A 334 HOH A 337 HOH A 342 CRYST1 37.650 41.200 59.966 90.00 90.00 90.00 P 21 21 21 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 0.026560 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016676 0.00000