HEADER TRANSPORT PROTEIN 06-SEP-22 8B01 TITLE CRYO-EM STRUCTURE OF THE TRIPARTITE ATP-INDEPENDENT PERIPLASMIC (TRAP) TITLE 2 TRANSPORTER SIAQM FROM PHOTOBACTERIUM PROFUNDUM IN A NANODISC COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TRAP-TYPE C4-DICARBOXYLATE TRANSPORT SYSTEM, SMALL COMPND 3 PERMEASE COMPONENT; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PUTATIVE TRAP-TYPE C4-DICARBOXYLATE TRANSPORT SYSTEM, LARGE COMPND 8 PERMEASE COMPONENT; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: MEGABODY C7HOPQ; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTOBACTERIUM PROFUNDUM SS9; SOURCE 3 ORGANISM_TAXID: 298386; SOURCE 4 STRAIN: SS9; SOURCE 5 GENE: VC1778, PBPRA2280; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: PHOTOBACTERIUM PROFUNDUM SS9; SOURCE 10 ORGANISM_TAXID: 298386; SOURCE 11 STRAIN: SS9; SOURCE 12 GENE: SMB20297, PBPRA2279; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI, SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 210, 32630; SOURCE 18 STRAIN: G27; SOURCE 19 GENE: HOPQ, HPG27_1120; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRAP, ELEVATOR, SECONDARY TRANSPORTER, SIALIC ACID, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.S.DAVIES,R.A.NORTH,R.C.J.DOBSON REVDAT 1 15-MAR-23 8B01 0 JRNL AUTH J.S.DAVIES,M.J.CURRIE,R.A.NORTH,M.SCALISE,J.D.WRIGHT, JRNL AUTH 2 J.M.COPPING,D.M.REMUS,A.GULATI,D.R.MORADO,S.A.JAMIESON, JRNL AUTH 3 M.C.NEWTON-VESTY,G.S.ABEYSEKERA,S.RAMASWAMY,R.FRIEMANN, JRNL AUTH 4 S.WAKATSUKI,J.R.ALLISON,C.INDIVERI,D.DREW,P.D.MACE, JRNL AUTH 5 R.C.J.DOBSON JRNL TITL STRUCTURE AND MECHANISM OF A TRIPARTITE ATP-INDEPENDENT JRNL TITL 2 PERIPLASMIC TRAP TRANSPORTER. JRNL REF NAT COMMUN V. 14 1120 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36849793 JRNL DOI 10.1038/S41467-023-36590-1 REMARK 2 REMARK 2 RESOLUTION. 3.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.030 REMARK 3 NUMBER OF PARTICLES : 499085 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8B01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125503. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SIAQM WITH MEGABODY; SIAQM; REMARK 245 MEGABODY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 8127 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 7090.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 154 REMARK 465 ASN A 155 REMARK 465 GLU A 156 REMARK 465 ASN A 157 REMARK 465 LYS A 158 REMARK 465 ASN A 159 REMARK 465 THR A 160 REMARK 465 SER A 161 REMARK 465 HIS A 162 REMARK 465 LEU A 163 REMARK 465 THR A 164 REMARK 465 ALA A 165 REMARK 465 CYS A 166 REMARK 465 ASP A 167 REMARK 465 ILE A 168 REMARK 465 ASN A 169 REMARK 465 GLU A 170 REMARK 465 GLN C -389 REMARK 465 VAL C -388 REMARK 465 GLN C -387 REMARK 465 LEU C -386 REMARK 465 GLN C -385 REMARK 465 GLU C -384 REMARK 465 SER C -383 REMARK 465 GLY C -382 REMARK 465 GLY C -381 REMARK 465 GLY C -380 REMARK 465 LEU C -379 REMARK 465 VAL C -378 REMARK 465 GLN C -377 REMARK 465 THR C -376 REMARK 465 LYS C -375 REMARK 465 THR C -374 REMARK 465 THR C -373 REMARK 465 THR C -372 REMARK 465 SER C -371 REMARK 465 VAL C -370 REMARK 465 ILE C -369 REMARK 465 ASP C -368 REMARK 465 THR C -367 REMARK 465 THR C -366 REMARK 465 ASN C -365 REMARK 465 ASP C -364 REMARK 465 ALA C -363 REMARK 465 GLN C -362 REMARK 465 ASN C -361 REMARK 465 LEU C -360 REMARK 465 LEU C -359 REMARK 465 THR C -358 REMARK 465 GLN C -357 REMARK 465 ALA C -356 REMARK 465 GLN C -355 REMARK 465 THR C -354 REMARK 465 ILE C -353 REMARK 465 VAL C -352 REMARK 465 ASN C -351 REMARK 465 THR C -350 REMARK 465 LEU C -349 REMARK 465 LYS C -348 REMARK 465 ASP C -347 REMARK 465 TYR C -346 REMARK 465 CYS C -345 REMARK 465 PRO C -344 REMARK 465 ILE C -343 REMARK 465 LEU C -342 REMARK 465 ILE C -341 REMARK 465 ALA C -340 REMARK 465 LYS C -339 REMARK 465 SER C -338 REMARK 465 SER C -337 REMARK 465 SER C -336 REMARK 465 SER C -335 REMARK 465 ASN C -334 REMARK 465 GLY C -333 REMARK 465 GLY C -332 REMARK 465 THR C -331 REMARK 465 ASN C -330 REMARK 465 ASN C -329 REMARK 465 ALA C -328 REMARK 465 ASN C -327 REMARK 465 THR C -326 REMARK 465 PRO C -325 REMARK 465 SER C -324 REMARK 465 TRP C -323 REMARK 465 GLN C -322 REMARK 465 THR C -321 REMARK 465 ALA C -320 REMARK 465 GLY C -319 REMARK 465 GLY C -318 REMARK 465 GLY C -317 REMARK 465 LYS C -316 REMARK 465 ASN C -315 REMARK 465 SER C -314 REMARK 465 CYS C -313 REMARK 465 ALA C -312 REMARK 465 THR C -311 REMARK 465 PHE C -310 REMARK 465 GLY C -309 REMARK 465 ALA C -308 REMARK 465 GLU C -307 REMARK 465 PHE C -306 REMARK 465 SER C -305 REMARK 465 ALA C -304 REMARK 465 ALA C -303 REMARK 465 SER C -302 REMARK 465 ASP C -301 REMARK 465 MET C -300 REMARK 465 ILE C -299 REMARK 465 ASN C -298 REMARK 465 ASN C -297 REMARK 465 ALA C -296 REMARK 465 GLN C -295 REMARK 465 LYS C -294 REMARK 465 ILE C -293 REMARK 465 VAL C -292 REMARK 465 GLN C -291 REMARK 465 GLU C -290 REMARK 465 THR C -289 REMARK 465 GLN C -288 REMARK 465 GLN C -287 REMARK 465 LEU C -286 REMARK 465 SER C -285 REMARK 465 ALA C -284 REMARK 465 ASN C -283 REMARK 465 GLN C -282 REMARK 465 PRO C -281 REMARK 465 LYS C -280 REMARK 465 ASN C -279 REMARK 465 ILE C -278 REMARK 465 THR C -277 REMARK 465 GLN C -276 REMARK 465 PRO C -275 REMARK 465 HIS C -274 REMARK 465 ASN C -273 REMARK 465 LEU C -272 REMARK 465 ASN C -271 REMARK 465 LEU C -270 REMARK 465 ASN C -269 REMARK 465 SER C -268 REMARK 465 PRO C -267 REMARK 465 SER C -266 REMARK 465 SER C -265 REMARK 465 LEU C -264 REMARK 465 THR C -263 REMARK 465 ALA C -262 REMARK 465 LEU C -261 REMARK 465 ALA C -260 REMARK 465 GLN C -259 REMARK 465 LYS C -258 REMARK 465 MET C -257 REMARK 465 LEU C -256 REMARK 465 LYS C -255 REMARK 465 ASN C -254 REMARK 465 ALA C -253 REMARK 465 GLN C -252 REMARK 465 SER C -251 REMARK 465 GLN C -250 REMARK 465 ALA C -249 REMARK 465 GLU C -248 REMARK 465 ILE C -247 REMARK 465 LEU C -246 REMARK 465 LYS C -245 REMARK 465 LEU C -244 REMARK 465 ALA C -243 REMARK 465 ASN C -242 REMARK 465 GLN C -241 REMARK 465 VAL C -240 REMARK 465 GLU C -239 REMARK 465 SER C -238 REMARK 465 ASP C -237 REMARK 465 PHE C -236 REMARK 465 ASN C -235 REMARK 465 LYS C -234 REMARK 465 LEU C -233 REMARK 465 SER C -232 REMARK 465 SER C -231 REMARK 465 GLY C -230 REMARK 465 HIS C -229 REMARK 465 LEU C -228 REMARK 465 LYS C -227 REMARK 465 ASP C -226 REMARK 465 TYR C -225 REMARK 465 ILE C -224 REMARK 465 GLY C -223 REMARK 465 LYS C -222 REMARK 465 CYS C -221 REMARK 465 ASP C -220 REMARK 465 ALA C -219 REMARK 465 SER C -218 REMARK 465 ALA C -217 REMARK 465 ILE C -216 REMARK 465 SER C -215 REMARK 465 SER C -214 REMARK 465 ALA C -213 REMARK 465 ASN C -212 REMARK 465 MET C -211 REMARK 465 THR C -210 REMARK 465 MET C -209 REMARK 465 GLN C -208 REMARK 465 ASN C -207 REMARK 465 GLN C -206 REMARK 465 LYS C -205 REMARK 465 ASN C -204 REMARK 465 ASN C -203 REMARK 465 TRP C -202 REMARK 465 GLY C -201 REMARK 465 ASN C -200 REMARK 465 GLY C -199 REMARK 465 CYS C -198 REMARK 465 ALA C -197 REMARK 465 GLY C -196 REMARK 465 VAL C -195 REMARK 465 GLU C -194 REMARK 465 GLU C -193 REMARK 465 THR C -192 REMARK 465 GLN C -191 REMARK 465 SER C -190 REMARK 465 LEU C -189 REMARK 465 LEU C -188 REMARK 465 LYS C -187 REMARK 465 THR C -186 REMARK 465 SER C -185 REMARK 465 ALA C -184 REMARK 465 ALA C -183 REMARK 465 ASP C -182 REMARK 465 PHE C -181 REMARK 465 ASN C -180 REMARK 465 ASN C -179 REMARK 465 GLN C -178 REMARK 465 THR C -177 REMARK 465 PRO C -176 REMARK 465 GLN C -175 REMARK 465 ILE C -174 REMARK 465 ASN C -173 REMARK 465 GLN C -172 REMARK 465 ALA C -171 REMARK 465 GLN C -170 REMARK 465 ASN C -169 REMARK 465 LEU C -168 REMARK 465 ALA C -167 REMARK 465 ASN C -166 REMARK 465 THR C -165 REMARK 465 LEU C -164 REMARK 465 ILE C -163 REMARK 465 GLN C -162 REMARK 465 GLU C -161 REMARK 465 LEU C -160 REMARK 465 GLY C -159 REMARK 465 ASN C -158 REMARK 465 ASN C -157 REMARK 465 ASP C -156 REMARK 465 THR C -155 REMARK 465 TYR C -154 REMARK 465 GLU C -153 REMARK 465 GLN C -152 REMARK 465 LEU C -151 REMARK 465 SER C -150 REMARK 465 ARG C -149 REMARK 465 LEU C -148 REMARK 465 LEU C -147 REMARK 465 THR C -146 REMARK 465 ASN C -145 REMARK 465 ASP C -144 REMARK 465 ASN C -143 REMARK 465 GLY C -142 REMARK 465 THR C -141 REMARK 465 ASN C -140 REMARK 465 SER C -139 REMARK 465 LYS C -138 REMARK 465 THR C -137 REMARK 465 SER C -136 REMARK 465 ALA C -135 REMARK 465 GLN C -134 REMARK 465 ALA C -133 REMARK 465 ILE C -132 REMARK 465 ASN C -131 REMARK 465 GLN C -130 REMARK 465 ALA C -129 REMARK 465 VAL C -128 REMARK 465 ASN C -127 REMARK 465 ASN C -126 REMARK 465 LEU C -125 REMARK 465 ASN C -124 REMARK 465 GLU C -123 REMARK 465 ARG C -122 REMARK 465 ALA C -121 REMARK 465 LYS C -120 REMARK 465 THR C -119 REMARK 465 LEU C -118 REMARK 465 ALA C -117 REMARK 465 GLY C -116 REMARK 465 GLY C -115 REMARK 465 THR C -114 REMARK 465 THR C -113 REMARK 465 ASN C -112 REMARK 465 SER C -111 REMARK 465 PRO C -110 REMARK 465 ALA C -109 REMARK 465 TYR C -108 REMARK 465 GLN C -107 REMARK 465 ALA C -106 REMARK 465 THR C -105 REMARK 465 LEU C -104 REMARK 465 LEU C -103 REMARK 465 ALA C -102 REMARK 465 LEU C -101 REMARK 465 ARG C -100 REMARK 465 SER C -99 REMARK 465 VAL C -98 REMARK 465 LEU C -97 REMARK 465 GLY C -96 REMARK 465 LEU C -95 REMARK 465 TRP C -94 REMARK 465 ASN C -93 REMARK 465 SER C -92 REMARK 465 MET C -91 REMARK 465 GLY C -90 REMARK 465 TYR C -89 REMARK 465 ALA C -88 REMARK 465 VAL C -87 REMARK 465 ILE C -86 REMARK 465 CYS C -85 REMARK 465 GLY C -84 REMARK 465 GLY C -83 REMARK 465 TYR C -82 REMARK 465 THR C -81 REMARK 465 LYS C -80 REMARK 465 SER C -79 REMARK 465 PRO C -78 REMARK 465 GLY C -77 REMARK 465 GLU C -76 REMARK 465 ASN C -75 REMARK 465 ASN C -74 REMARK 465 GLN C -73 REMARK 465 LYS C -72 REMARK 465 ASP C -71 REMARK 465 PHE C -70 REMARK 465 HIS C -69 REMARK 465 TYR C -68 REMARK 465 THR C -67 REMARK 465 ASP C -66 REMARK 465 GLU C -65 REMARK 465 ASN C -64 REMARK 465 GLY C -63 REMARK 465 ASN C -62 REMARK 465 GLY C -61 REMARK 465 THR C -60 REMARK 465 THR C -59 REMARK 465 ILE C -58 REMARK 465 ASN C -57 REMARK 465 CYS C -56 REMARK 465 GLY C -55 REMARK 465 GLY C -54 REMARK 465 SER C -53 REMARK 465 THR C -52 REMARK 465 ASN C -51 REMARK 465 SER C -50 REMARK 465 ASN C -49 REMARK 465 GLY C -48 REMARK 465 THR C -47 REMARK 465 HIS C -46 REMARK 465 SER C -45 REMARK 465 TYR C -44 REMARK 465 ASN C -43 REMARK 465 GLY C -42 REMARK 465 THR C -41 REMARK 465 ASN C -40 REMARK 465 THR C -39 REMARK 465 LEU C -38 REMARK 465 LYS C -37 REMARK 465 ALA C -36 REMARK 465 ASP C -35 REMARK 465 LYS C -34 REMARK 465 ASN C -33 REMARK 465 VAL C -32 REMARK 465 SER C -31 REMARK 465 LEU C -30 REMARK 465 SER C -29 REMARK 465 ILE C -28 REMARK 465 GLU C -27 REMARK 465 GLN C -26 REMARK 465 TYR C -25 REMARK 465 GLU C -24 REMARK 465 LYS C -23 REMARK 465 ILE C -22 REMARK 465 HIS C -21 REMARK 465 GLU C -20 REMARK 465 ALA C -19 REMARK 465 TYR C -18 REMARK 465 GLN C -17 REMARK 465 ILE C -16 REMARK 465 LEU C -15 REMARK 465 SER C -14 REMARK 465 LYS C -13 REMARK 465 ALA C -12 REMARK 465 LEU C -11 REMARK 465 LYS C -10 REMARK 465 GLN C -9 REMARK 465 ALA C -8 REMARK 465 GLY C -7 REMARK 465 LEU C -6 REMARK 465 ALA C -5 REMARK 465 PRO C -4 REMARK 465 LEU C -3 REMARK 465 ASN C -2 REMARK 465 SER C -1 REMARK 465 LYS C 0 REMARK 465 GLY C 1 REMARK 465 GLU C 2 REMARK 465 LYS C 3 REMARK 465 LEU C 4 REMARK 465 GLU C 5 REMARK 465 ALA C 6 REMARK 465 HIS C 7 REMARK 465 VAL C 8 REMARK 465 THR C 9 REMARK 465 THR C 10 REMARK 465 SER C 11 REMARK 465 LYS C 12 REMARK 465 TYR C 13 REMARK 465 SER C 118 REMARK 465 LEU C 119 REMARK 465 GLU C 120 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 LEU B 91 -5.50 69.25 REMARK 500 MET B 105 -64.91 -98.21 REMARK 500 PHE B 327 13.97 -140.38 REMARK 500 ALA C 24 -129.48 59.52 REMARK 500 PRO C 87 2.75 -65.05 REMARK 500 TRP C 108 89.16 -150.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PTY B 510 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 NA B 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 103 O REMARK 620 2 SER B 106 O 85.8 REMARK 620 3 GLY B 145 O 121.6 133.1 REMARK 620 4 VAL B 148 O 104.1 138.4 75.7 REMARK 620 5 PRO B 150 O 136.6 76.8 98.6 68.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 325 O REMARK 620 2 GLY B 366 O 92.6 REMARK 620 3 THR B 369 O 153.1 104.0 REMARK 620 4 THR B 369 OG1 97.6 61.8 72.8 REMARK 620 5 MET B 372 O 102.9 134.2 80.7 152.5 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13968 RELATED DB: EMDB REMARK 900 7QHA CONTAINS THE SAME PROTEIN COMPLEX IN AMPHIPOL, INSTEAD OF A REMARK 900 NANODISC. REMARK 900 RELATED ID: EMD-15775 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE TRIPARTITE ATP-INDEPENDENT PERIPLASMIC REMARK 900 (TRAP) TRANSPORTER SIAQM FROM PHOTOBACTERIUM PROFUNDUM IN A NANODISC DBREF 8B01 A 1 169 UNP Q6LPW0 Q6LPW0_PHOPR 1 169 DBREF 8B01 B 1 426 UNP Q6LPW1 Q6LPW1_PHOPR 1 426 DBREF 8B01 C -377 -157 UNP B5Z8H1 B5Z8H1_HELPG 226 446 DBREF 8B01 C -156 120 PDB 8B01 8B01 -156 120 SEQADV 8B01 GLU A 170 UNP Q6LPW0 EXPRESSION TAG SEQADV 8B01 LEU B 427 UNP Q6LPW1 EXPRESSION TAG SEQADV 8B01 GLN C -389 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 VAL C -388 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 GLN C -387 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 LEU C -386 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 GLN C -385 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 GLU C -384 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 SER C -383 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 GLY C -382 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 GLY C -381 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 GLY C -380 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 LEU C -379 UNP B5Z8H1 EXPRESSION TAG SEQADV 8B01 VAL C -378 UNP B5Z8H1 EXPRESSION TAG SEQRES 1 A 170 MET PHE ARG LYS ILE ILE ASP ASN ILE GLU GLU ILE ILE SEQRES 2 A 170 THR VAL PRO LEU MET ILE ALA LEU LEU CYS ILE LEU THR SEQRES 3 A 170 TRP GLN ILE SER SER ARG TRP LEU PHE ASP SER PRO SER SEQRES 4 A 170 LEU TRP SER GLU GLU LEU ALA ARG VAL LEU PHE LEU HIS SEQRES 5 A 170 MET ALA ILE ILE GLY GLY ALA ILE ALA ILE LYS LYS ASP SEQRES 6 A 170 ASP HIS VAL LYS ILE THR PHE PHE SER ASP LYS LEU PRO SEQRES 7 A 170 ARG ASN PHE ARG TYR SER LEU LEU PHE ALA LEU GLU LEU SEQRES 8 A 170 LEU VAL LEU ILE THR ILE VAL ALA MET ILE TYR TYR GLY SEQRES 9 A 170 TYR ALA HIS VAL GLN ARG THR ALA PHE PHE GLU LEU ILE SEQRES 10 A 170 THR LEU GLY ILE SER SER SER TRP MET THR TYR ALA LEU SEQRES 11 A 170 PRO VAL GLY GLY CYS PHE MET LEU VAL ARG GLN CYS GLN SEQRES 12 A 170 LYS LEU TYR PHE VAL LEU ILE ASP TRP ARG ILE ASN GLU SEQRES 13 A 170 ASN LYS ASN THR SER HIS LEU THR ALA CYS ASP ILE ASN SEQRES 14 A 170 GLU SEQRES 1 B 427 MET PHE THR SER ILE VAL GLY TRP LEU GLY LEU LEU PHE SEQRES 2 B 427 ALA GLY MET PRO VAL GLY PHE SER LEU ILE PHE VAL GLY SEQRES 3 B 427 LEU ALA PHE LEU VAL LEU THR GLU SER THR GLY ILE ASN SEQRES 4 B 427 PHE ALA ALA GLN GLN MET ILE GLY GLY LEU ASP ASN PHE SEQRES 5 B 427 THR LEU LEU ALA VAL PRO PHE PHE VAL LEU THR GLY HIS SEQRES 6 B 427 LEU MET ASN SER ALA GLY ILE THR GLU ARG ILE PHE ASN SEQRES 7 B 427 PHE ALA LYS ALA MET VAL GLY HIS ILE THR GLY SER LEU SEQRES 8 B 427 GLY HIS VAL ASN ILE LEU ALA SER LEU LEU PHE SER GLY SEQRES 9 B 427 MET SER GLY SER ALA LEU ALA ASP ALA GLY GLY LEU GLY SEQRES 10 B 427 GLN LEU GLU ILE LYS SER MET ARG ASP ALA LYS TYR ASP SEQRES 11 B 427 ASP ASP PHE ALA GLY GLY LEU THR ALA ALA SER CYS ILE SEQRES 12 B 427 ILE GLY PRO LEU VAL PRO PRO SER ILE PRO LEU VAL ILE SEQRES 13 B 427 TYR GLY VAL VAL SER ASN THR SER ILE GLY ALA LEU PHE SEQRES 14 B 427 LEU ALA GLY ALA ILE PRO GLY LEU LEU CYS CYS ILE ALA SEQRES 15 B 427 LEU CYS ILE MET THR TYR PHE ILE ALA LYS LYS ARG GLY SEQRES 16 B 427 TYR MET THR LEU PRO ARG ALA SER ARG LYS GLU ARG LEU SEQRES 17 B 427 ILE ALA PHE ARG ASP ALA PHE LEU SER LEU LEU THR PRO SEQRES 18 B 427 PHE ILE ILE ILE GLY GLY ILE PHE SER GLY LYS PHE THR SEQRES 19 B 427 PRO THR GLU ALA ALA ILE ILE SER SER LEU TYR ALA LEU SEQRES 20 B 427 PHE LEU GLY THR VAL VAL TYR LYS SER LEU THR MET ASP SEQRES 21 B 427 LYS PHE ILE LYS LEU VAL GLN GLU THR VAL THR THR THR SEQRES 22 B 427 SER VAL VAL ALA LEU MET VAL MET GLY VAL THR VAL PHE SEQRES 23 B 427 GLY TRP ILE VAL ALA ARG GLU GLN LEU PRO GLN GLN LEU SEQRES 24 B 427 ALA GLU LEU PHE LEU SER ILE SER ASP ASN PRO LEU ILE SEQRES 25 B 427 LEU LEU LEU LEU ILE ASN LEU LEU LEU LEU PHE LEU GLY SEQRES 26 B 427 THR PHE ILE GLU SER LEU ALA LEU LEU LEU LEU LEU VAL SEQRES 27 B 427 PRO PHE LEU VAL PRO VAL ALA THR SER VAL GLY ILE ASP SEQRES 28 B 427 PRO VAL HIS PHE GLY VAL MET ALA ILE LEU ASN LEU MET SEQRES 29 B 427 ILE GLY ILE LEU THR PRO PRO MET GLY MET ALA LEU TYR SEQRES 30 B 427 VAL VAL SER LYS VAL GLY ASN ILE PRO PHE HIS VAL LEU SEQRES 31 B 427 THR ARG GLY VAL LEU PRO LEU LEU VAL PRO LEU PHE ILE SEQRES 32 B 427 VAL LEU GLY LEU ILE ILE VAL PHE PRO GLN ILE THR LEU SEQRES 33 B 427 PHE LEU PRO GLN LEU VAL LEU GLY TYR GLY LEU SEQRES 1 C 510 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 510 THR LYS THR THR THR SER VAL ILE ASP THR THR ASN ASP SEQRES 3 C 510 ALA GLN ASN LEU LEU THR GLN ALA GLN THR ILE VAL ASN SEQRES 4 C 510 THR LEU LYS ASP TYR CYS PRO ILE LEU ILE ALA LYS SER SEQRES 5 C 510 SER SER SER ASN GLY GLY THR ASN ASN ALA ASN THR PRO SEQRES 6 C 510 SER TRP GLN THR ALA GLY GLY GLY LYS ASN SER CYS ALA SEQRES 7 C 510 THR PHE GLY ALA GLU PHE SER ALA ALA SER ASP MET ILE SEQRES 8 C 510 ASN ASN ALA GLN LYS ILE VAL GLN GLU THR GLN GLN LEU SEQRES 9 C 510 SER ALA ASN GLN PRO LYS ASN ILE THR GLN PRO HIS ASN SEQRES 10 C 510 LEU ASN LEU ASN SER PRO SER SER LEU THR ALA LEU ALA SEQRES 11 C 510 GLN LYS MET LEU LYS ASN ALA GLN SER GLN ALA GLU ILE SEQRES 12 C 510 LEU LYS LEU ALA ASN GLN VAL GLU SER ASP PHE ASN LYS SEQRES 13 C 510 LEU SER SER GLY HIS LEU LYS ASP TYR ILE GLY LYS CYS SEQRES 14 C 510 ASP ALA SER ALA ILE SER SER ALA ASN MET THR MET GLN SEQRES 15 C 510 ASN GLN LYS ASN ASN TRP GLY ASN GLY CYS ALA GLY VAL SEQRES 16 C 510 GLU GLU THR GLN SER LEU LEU LYS THR SER ALA ALA ASP SEQRES 17 C 510 PHE ASN ASN GLN THR PRO GLN ILE ASN GLN ALA GLN ASN SEQRES 18 C 510 LEU ALA ASN THR LEU ILE GLN GLU LEU GLY ASN ASN ASP SEQRES 19 C 510 THR TYR GLU GLN LEU SER ARG LEU LEU THR ASN ASP ASN SEQRES 20 C 510 GLY THR ASN SER LYS THR SER ALA GLN ALA ILE ASN GLN SEQRES 21 C 510 ALA VAL ASN ASN LEU ASN GLU ARG ALA LYS THR LEU ALA SEQRES 22 C 510 GLY GLY THR THR ASN SER PRO ALA TYR GLN ALA THR LEU SEQRES 23 C 510 LEU ALA LEU ARG SER VAL LEU GLY LEU TRP ASN SER MET SEQRES 24 C 510 GLY TYR ALA VAL ILE CYS GLY GLY TYR THR LYS SER PRO SEQRES 25 C 510 GLY GLU ASN ASN GLN LYS ASP PHE HIS TYR THR ASP GLU SEQRES 26 C 510 ASN GLY ASN GLY THR THR ILE ASN CYS GLY GLY SER THR SEQRES 27 C 510 ASN SER ASN GLY THR HIS SER TYR ASN GLY THR ASN THR SEQRES 28 C 510 LEU LYS ALA ASP LYS ASN VAL SER LEU SER ILE GLU GLN SEQRES 29 C 510 TYR GLU LYS ILE HIS GLU ALA TYR GLN ILE LEU SER LYS SEQRES 30 C 510 ALA LEU LYS GLN ALA GLY LEU ALA PRO LEU ASN SER LYS SEQRES 31 C 510 GLY GLU LYS LEU GLU ALA HIS VAL THR THR SER LYS TYR SEQRES 32 C 510 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 33 C 510 ASN ILE PHE ASP ARG GLY TYR MET GLY TRP TYR ARG GLN SEQRES 34 C 510 ALA PRO GLY LYS GLU ARG GLU LEU VAL ALA GLY ILE SER SEQRES 35 C 510 TYR GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 36 C 510 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 37 C 510 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 38 C 510 VAL TYR TYR CYS ALA ALA TYR PRO LEU TYR ASP ASP PRO SEQRES 39 C 510 TYR TYR TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SEQRES 40 C 510 SER LEU GLU HET OCT A 201 8 HET PTY A 202 50 HET TWT A 203 22 HET D10 A 204 10 HET NA B 501 1 HET NA B 502 1 HET OCT B 503 8 HET OCT B 504 8 HET OCT B 505 8 HET OCT B 506 8 HET OCT B 507 8 HET TRD B 508 13 HET D10 B 509 10 HET PTY B 510 37 HET HEX B 511 6 HETNAM OCT N-OCTANE HETNAM PTY PHOSPHATIDYLETHANOLAMINE HETNAM TWT DOCOSANE HETNAM D10 DECANE HETNAM NA SODIUM ION HETNAM TRD TRIDECANE HETNAM HEX HEXANE HETSYN TRD LIPID FRAGMENT FORMUL 4 OCT 6(C8 H18) FORMUL 5 PTY 2(C40 H80 N O8 P) FORMUL 6 TWT C22 H46 FORMUL 7 D10 2(C10 H22) FORMUL 8 NA 2(NA 1+) FORMUL 15 TRD C13 H28 FORMUL 18 HEX C6 H14 HELIX 1 AA1 PHE A 2 ASN A 8 1 7 HELIX 2 AA2 ASN A 8 PHE A 35 1 28 HELIX 3 AA3 TRP A 41 LYS A 64 1 24 HELIX 4 AA4 PHE A 73 LEU A 77 5 5 HELIX 5 AA5 PRO A 78 THR A 111 1 34 HELIX 6 AA6 SER A 123 TYR A 128 1 6 HELIX 7 AA7 TYR A 128 TRP A 152 1 25 HELIX 8 AA8 PHE B 2 GLY B 15 1 14 HELIX 9 AA9 PRO B 17 THR B 33 1 17 HELIX 10 AB1 SER B 35 ASN B 39 5 5 HELIX 11 AB2 PHE B 40 ASP B 50 1 11 HELIX 12 AB3 PHE B 52 LEU B 54 5 3 HELIX 13 AB4 LEU B 55 ALA B 70 1 16 HELIX 14 AB5 GLY B 71 GLY B 85 1 15 HELIX 15 AB6 GLY B 92 GLY B 104 1 13 HELIX 16 AB7 SER B 108 ALA B 127 1 20 HELIX 17 AB8 ASP B 130 CYS B 142 1 13 HELIX 18 AB9 ILE B 143 VAL B 148 1 6 HELIX 19 AC1 SER B 151 ASN B 162 1 12 HELIX 20 AC2 SER B 164 GLY B 172 1 9 HELIX 21 AC3 GLY B 172 GLY B 195 1 24 HELIX 22 AC4 SER B 203 ASP B 213 1 11 HELIX 23 AC5 PHE B 215 SER B 217 5 3 HELIX 24 AC6 LEU B 218 SER B 230 1 13 HELIX 25 AC7 THR B 234 VAL B 252 1 19 HELIX 26 AC8 THR B 258 ARG B 292 1 35 HELIX 27 AC9 GLN B 294 SER B 307 1 14 HELIX 28 AD1 ASN B 309 GLY B 325 1 17 HELIX 29 AD2 GLU B 329 LEU B 337 1 9 HELIX 30 AD3 LEU B 337 GLY B 349 1 13 HELIX 31 AD4 ASP B 351 ILE B 367 1 17 HELIX 32 AD5 GLY B 373 ASN B 384 1 12 HELIX 33 AD6 PRO B 386 LEU B 395 1 10 HELIX 34 AD7 LEU B 398 PHE B 411 1 14 HELIX 35 AD8 PRO B 412 LEU B 423 1 12 SHEET 1 AA1 2 GLU A 115 LEU A 116 0 SHEET 2 AA1 2 ILE A 121 SER A 122 -1 O ILE A 121 N LEU A 116 SHEET 1 AA2 3 SER C 17 CYS C 22 0 SHEET 2 AA2 3 THR C 77 ASN C 83 -1 O MET C 82 N LEU C 18 SHEET 3 AA2 3 PHE C 67 ASP C 72 -1 N SER C 70 O TYR C 79 SHEET 1 AA3 5 THR C 57 TYR C 59 0 SHEET 2 AA3 5 ARG C 45 ILE C 51 -1 N GLY C 50 O TYR C 58 SHEET 3 AA3 5 MET C 34 GLN C 39 -1 N TRP C 36 O ALA C 49 SHEET 4 AA3 5 ALA C 91 ALA C 96 -1 O TYR C 94 N TYR C 37 SHEET 5 AA3 5 THR C 112 VAL C 114 -1 O THR C 112 N TYR C 93 SSBOND 1 CYS C 22 CYS C 95 1555 1555 2.04 LINK O SER B 103 NA NA B 501 1555 1555 2.42 LINK O SER B 106 NA NA B 501 1555 1555 2.54 LINK O GLY B 145 NA NA B 501 1555 1555 2.28 LINK O VAL B 148 NA NA B 501 1555 1555 2.52 LINK O PRO B 150 NA NA B 501 1555 1555 2.70 LINK O GLY B 325 NA NA B 502 1555 1555 2.97 LINK O GLY B 366 NA NA B 502 1555 1555 2.49 LINK O THR B 369 NA NA B 502 1555 1555 2.53 LINK OG1 THR B 369 NA NA B 502 1555 1555 2.67 LINK O MET B 372 NA NA B 502 1555 1555 2.35 CISPEP 1 PRO B 149 PRO B 150 0 0.57 CISPEP 2 PRO B 370 PRO B 371 0 0.22 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000