HEADER TRANSPORT PROTEIN 01-JUN-17 5XPD TITLE SUGAR TRANSPORTER OF ATSWEET13 IN INWARD-FACING STATE WITH A SUBSTRATE TITLE 2 ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_TAXID: 3702; SOURCE 4 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS SWEETS SUGAR TRANSPORTER COMPLEX, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.HAN,X.J.ZHANG REVDAT 3 22-NOV-23 5XPD 1 REMARK REVDAT 2 04-OCT-17 5XPD 1 JRNL REVDAT 1 13-SEP-17 5XPD 0 JRNL AUTH L.HAN,Y.P.ZHU,M.LIU,Y.ZHOU,G.Y.LU,L.LAN,X.P.WANG,Y.F.ZHAO, JRNL AUTH 2 X.C.ZHANG JRNL TITL MOLECULAR MECHANISM OF SUBSTRATE RECOGNITION AND TRANSPORT JRNL TITL 2 BY THE ATSWEET13 SUGAR TRANSPORTER JRNL REF PROC. NATL. ACAD. SCI. V. 114 10089 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28878024 JRNL DOI 10.1073/PNAS.1709241114 REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1819 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) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 9229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.190 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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 36.6874 - 5.3281 0.95 1200 142 0.2350 0.2602 REMARK 3 2 5.3281 - 4.2310 0.97 1200 130 0.2264 0.2473 REMARK 3 3 4.2310 - 3.6968 0.98 1195 139 0.2320 0.2863 REMARK 3 4 3.6968 - 3.3590 0.99 1188 137 0.2426 0.2836 REMARK 3 5 3.3590 - 3.1184 0.97 1186 128 0.2737 0.3396 REMARK 3 6 3.1184 - 2.9346 0.97 1184 131 0.2984 0.3133 REMARK 3 7 2.9346 - 2.7877 0.93 1136 133 0.3250 0.3609 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.260 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 : 0.005 2180 REMARK 3 ANGLE : 0.962 2968 REMARK 3 CHIRALITY : 0.033 347 REMARK 3 PLANARITY : 0.005 359 REMARK 3 DIHEDRAL : 12.981 755 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 5XPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300003934. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9248 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.788 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 (%) : 96.3 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.8000 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 5CTG AND 1FHH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES (PH 5.9), 38% (W/V) PEG 600, REMARK 280 100MM KH2PO4, LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 37.89000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.41550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.89000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.41550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 GLU A 275 REMARK 465 GLU A 276 REMARK 465 GLU A 277 REMARK 465 ASN A 278 REMARK 465 LEU A 279 REMARK 465 TYR A 280 REMARK 465 PHE A 281 REMARK 465 GLN A 282 REMARK 465 GLY A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 HIS A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 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 GLU A 41 CG CD OE1 OE2 REMARK 470 GLN A 222 CG CD OE1 NE2 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 GLU A 41 -126.13 49.90 REMARK 500 ASP A 66 -120.07 54.82 REMARK 500 PHE A 111 -68.96 -90.30 REMARK 500 TYR A 216 -70.10 -59.24 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 DCM A 301 DBREF 5XPD A 1 293 PDB 5XPD 5XPD 1 293 SEQRES 1 A 293 MET ALA LEU THR ASN ASN LEU TRP ALA PHE VAL PHE GLY SEQRES 2 A 293 ILE LEU GLY ASN ILE ILE SER PHE VAL LEU PHE LEU ALA SEQRES 3 A 293 PRO VAL PRO THR PHE VAL ARG ILE CYS LYS LYS LYS SER SEQRES 4 A 293 THR GLU GLY PHE GLN SER LEU PRO TYR VAL SER ALA LEU SEQRES 5 A 293 PHE ASN ALA MET LEU TRP ILE TYR TYR ALA MET GLN LYS SEQRES 6 A 293 ASP GLY THR ALA PHE LEU LEU ILE THR ILE ASN ALA PHE SEQRES 7 A 293 GLY CYS VAL ILE GLU THR ILE TYR ILE VAL LEU PHE VAL SEQRES 8 A 293 SER TYR ALA ASN LYS LYS THR ARG ILE SER THR LEU LYS SEQRES 9 A 293 VAL LEU GLY LEU LEU ASN PHE LEU GLY PHE ALA ALA ILE SEQRES 10 A 293 VAL LEU VAL CYS GLU LEU LEU THR LYS GLY SER THR ARG SEQRES 11 A 293 GLU LYS VAL LEU GLY GLY ILE CYS VAL GLY PHE SER VAL SEQRES 12 A 293 SER MET PHE ALA ALA PRO LEU SER ILE MET ARG VAL VAL SEQRES 13 A 293 VAL ARG THR ARG SER VAL GLU PHE MET PRO PHE SER LEU SEQRES 14 A 293 SER LEU PHE LEU THR ILE ASN ALA VAL THR TRP LEU PHE SEQRES 15 A 293 TYR GLY LEU ALA ILE LYS ASP PHE TYR VAL ALA LEU PRO SEQRES 16 A 293 ASN VAL LEU GLY ALA PHE LEU GLY ALA VAL GLN MET ILE SEQRES 17 A 293 LEU TYR ILE ILE PHE LYS TYR TYR LYS THR PRO VAL ALA SEQRES 18 A 293 GLN MET LYS LYS TYR THR CYS THR VAL CYS GLY TYR ILE SEQRES 19 A 293 TYR ASN PRO GLU ASP GLY ASP PRO ASP ASN GLY VAL ASN SEQRES 20 A 293 PRO GLY THR ASP PHE LYS ASP ILE PRO ASP ASP TRP VAL SEQRES 21 A 293 CYS PRO LEU CYS GLY VAL GLY LYS ASP GLN PHE GLU GLU SEQRES 22 A 293 VAL GLU GLU GLU ASN LEU TYR PHE GLN GLY HIS HIS HIS SEQRES 23 A 293 HIS HIS HIS HIS HIS HIS HIS HET DCM A 301 20 HETNAM DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE FORMUL 2 DCM C9 H14 N3 O7 P HELIX 1 AA1 ASN A 6 LEU A 25 1 20 HELIX 2 AA2 PRO A 27 LYS A 38 1 12 HELIX 3 AA3 SER A 45 ASP A 66 1 22 HELIX 4 AA4 GLY A 67 ALA A 69 5 3 HELIX 5 AA5 PHE A 70 TYR A 93 1 24 HELIX 6 AA6 ASN A 95 LEU A 109 1 15 HELIX 7 AA7 PHE A 111 THR A 125 1 15 HELIX 8 AA8 LYS A 126 MET A 145 1 20 HELIX 9 AA9 PHE A 146 ARG A 160 1 15 HELIX 10 AB1 PRO A 166 ILE A 187 1 22 HELIX 11 AB2 ASP A 189 LYS A 214 1 26 HELIX 12 AB3 PRO A 219 MET A 223 5 5 HELIX 13 AB4 ASP A 241 GLY A 245 5 5 HELIX 14 AB5 ASP A 251 ILE A 255 5 5 HELIX 15 AB6 GLY A 267 ASP A 269 5 3 SHEET 1 AA1 3 ILE A 234 TYR A 235 0 SHEET 2 AA1 3 TYR A 226 CYS A 228 -1 N TYR A 226 O TYR A 235 SHEET 3 AA1 3 PHE A 271 GLU A 273 -1 O GLU A 272 N THR A 227 SITE 1 AC1 7 SER A 20 LEU A 23 PHE A 24 ILE A 75 SITE 2 AC1 7 ASN A 176 PRO A 195 ASN A 196 CRYST1 75.780 42.831 116.553 90.00 93.85 90.00 C 1 2 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 0.013196 0.000000 0.000889 0.00000 SCALE2 0.000000 0.023348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008599 0.00000