HEADER PLANT PROTEIN 25-SEP-18 6IGI TITLE CRYSTAL STRUCTURE OF FT CONDITION 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FLOWERING LOCUS T; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-168; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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: FT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FLOWERING CONTROL, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WATANABE,Y.NAKAMURA,K.KANEHARA,K.INABA REVDAT 2 22-NOV-23 6IGI 1 REMARK REVDAT 1 25-DEC-19 6IGI 0 JRNL AUTH Y.NAKAMURA,Y.C.LIN,S.WATANABE,Y.C.LIU,K.KATSUYAMA, JRNL AUTH 2 K.KANEHARA,K.INABA JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF ARABIDOPSIS FLOWERING JRNL TITL 2 LOCUS T ILLUMINATES ITS PHOSPHOLIPID-BINDING SITE IN JRNL TITL 3 FLOWERING. JRNL REF ISCIENCE V. 21 577 2019 JRNL REFN ESSN 2589-0042 JRNL PMID 31726375 JRNL DOI 10.1016/J.ISCI.2019.10.045 REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 33428 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1634 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 30.0100 - 3.0400 1.00 2842 117 0.1541 0.1854 REMARK 3 2 3.0400 - 2.4200 1.00 2720 130 0.1467 0.1756 REMARK 3 3 2.4200 - 2.1100 1.00 2649 152 0.1334 0.1672 REMARK 3 4 2.1100 - 1.9200 1.00 2643 149 0.1371 0.1481 REMARK 3 5 1.9200 - 1.7800 1.00 2643 128 0.1455 0.2037 REMARK 3 6 1.7800 - 1.6700 1.00 2641 126 0.1534 0.1532 REMARK 3 7 1.6700 - 1.5900 1.00 2634 139 0.1649 0.1663 REMARK 3 8 1.5900 - 1.5200 1.00 2611 143 0.1834 0.2170 REMARK 3 9 1.5200 - 1.4600 1.00 2626 135 0.2087 0.2097 REMARK 3 10 1.4600 - 1.4100 1.00 2615 140 0.2320 0.2652 REMARK 3 11 1.4100 - 1.3700 1.00 2602 150 0.2467 0.2749 REMARK 3 12 1.3700 - 1.3300 0.98 2568 125 0.2620 0.3186 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) : 0.131 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.02 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 : 0.011 1394 REMARK 3 ANGLE : 1.170 1913 REMARK 3 CHIRALITY : 0.095 210 REMARK 3 PLANARITY : 0.009 259 REMARK 3 DIHEDRAL : 3.094 813 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 7 THROUGH 168) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2861 -10.4140 10.7855 REMARK 3 T TENSOR REMARK 3 T11: 0.0737 T22: 0.0653 REMARK 3 T33: 0.0807 T12: 0.0018 REMARK 3 T13: -0.0116 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 1.3115 L22: 0.8791 REMARK 3 L33: 1.2360 L12: 0.1532 REMARK 3 L13: -0.1752 L23: 0.2471 REMARK 3 S TENSOR REMARK 3 S11: 0.0220 S12: -0.0103 S13: -0.1357 REMARK 3 S21: 0.0294 S22: 0.0225 S23: -0.1236 REMARK 3 S31: 0.0390 S32: 0.0915 S33: -0.0254 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 6IGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1300009104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33436 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 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: MOLREP REMARK 200 STARTING MODEL: 1WKP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ISOPROPANOL,PEG3350 AND AMMONIUM REMARK 280 CITRATE/CITRIC ACID, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 24.24100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.45400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.76850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.45400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.24100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.76850 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 ILE A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ILE A 3 REMARK 465 ASN A 4 REMARK 465 ILE A 5 REMARK 465 ARG A 6 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 13 NE CZ NH1 NH2 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 457 O HOH A 475 2.19 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 326 O HOH A 479 2444 2.12 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 THR A 97 -119.10 -109.33 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 EDO A 201 DBREF 6IGI A 1 168 UNP Q9SXZ2 FT_ARATH 1 168 SEQADV 6IGI ILE A -2 UNP Q9SXZ2 EXPRESSION TAG SEQADV 6IGI SER A -1 UNP Q9SXZ2 EXPRESSION TAG SEQADV 6IGI HIS A 0 UNP Q9SXZ2 EXPRESSION TAG SEQADV 6IGI SER A 107 UNP Q9SXZ2 CYS 107 ENGINEERED MUTATION SEQADV 6IGI SER A 164 UNP Q9SXZ2 CYS 164 ENGINEERED MUTATION SEQRES 1 A 171 ILE SER HIS MET SER ILE ASN ILE ARG ASP PRO LEU ILE SEQRES 2 A 171 VAL SER ARG VAL VAL GLY ASP VAL LEU ASP PRO PHE ASN SEQRES 3 A 171 ARG SER ILE THR LEU LYS VAL THR TYR GLY GLN ARG GLU SEQRES 4 A 171 VAL THR ASN GLY LEU ASP LEU ARG PRO SER GLN VAL GLN SEQRES 5 A 171 ASN LYS PRO ARG VAL GLU ILE GLY GLY GLU ASP LEU ARG SEQRES 6 A 171 ASN PHE TYR THR LEU VAL MET VAL ASP PRO ASP VAL PRO SEQRES 7 A 171 SER PRO SER ASN PRO HIS LEU ARG GLU TYR LEU HIS TRP SEQRES 8 A 171 LEU VAL THR ASP ILE PRO ALA THR THR GLY THR THR PHE SEQRES 9 A 171 GLY ASN GLU ILE VAL SER TYR GLU ASN PRO SER PRO THR SEQRES 10 A 171 ALA GLY ILE HIS ARG VAL VAL PHE ILE LEU PHE ARG GLN SEQRES 11 A 171 LEU GLY ARG GLN THR VAL TYR ALA PRO GLY TRP ARG GLN SEQRES 12 A 171 ASN PHE ASN THR ARG GLU PHE ALA GLU ILE TYR ASN LEU SEQRES 13 A 171 GLY LEU PRO VAL ALA ALA VAL PHE TYR ASN SER GLN ARG SEQRES 14 A 171 GLU SER HET EDO A 201 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 HOH *201(H2 O) HELIX 1 AA1 ASP A 7 SER A 12 1 6 HELIX 2 AA2 ARG A 13 VAL A 18 1 6 HELIX 3 AA3 ARG A 44 VAL A 48 5 5 HELIX 4 AA4 GLY A 98 GLY A 102 5 5 HELIX 5 AA5 ASN A 143 TYR A 151 1 9 SHEET 1 AA1 3 ARG A 35 GLU A 36 0 SHEET 2 AA1 3 LEU A 28 TYR A 32 -1 N TYR A 32 O ARG A 35 SHEET 3 AA1 3 ARG A 53 ILE A 56 -1 O GLU A 55 N LYS A 29 SHEET 1 AA2 6 LEU A 41 ASP A 42 0 SHEET 2 AA2 6 ALA A 158 SER A 164 1 O ASN A 163 N LEU A 41 SHEET 3 AA2 6 HIS A 118 ARG A 126 -1 N PHE A 122 O VAL A 160 SHEET 4 AA2 6 PHE A 64 ASP A 71 -1 N VAL A 70 O VAL A 121 SHEET 5 AA2 6 TYR A 85 PRO A 94 -1 O VAL A 90 N LEU A 67 SHEET 6 AA2 6 ASN A 103 VAL A 106 -1 O ASN A 103 N THR A 91 CISPEP 1 VAL A 74 PRO A 75 0 0.03 CISPEP 2 ARG A 83 GLU A 84 0 -3.84 SITE 1 AC1 7 ARG A 35 GLN A 47 GLU A 59 GLU A 104 SITE 2 AC1 7 ILE A 105 HOH A 356 HOH A 358 CRYST1 48.482 51.537 56.908 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 0.020626 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019404 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017572 0.00000