HEADER TRANSPORT PROTEIN 25-MAR-22 7ZC2 TITLE DIPEPTIDE AND TRIPEPTIDE PERMEASE C (DTPC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINO ACID/PEPTIDE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DI/TRIPEPTIDE PERMEASE YJDL,DIPEPTIDE AND TRIPEPTIDE COMPND 5 PERMEASE,DIPEPTIDE AND TRIPEPTIDE PERMEASE D,DIPEPTIDE/TRIPEPTIDE COMPND 6 PERMEASE DTPC,MFS TRANSPORTER,PEPTIDE PERMEASE,PROBABLE DIPEPTIDE AND COMPND 7 TRIPEPTIDE PERMEASE YJDL,PUTATIVE DIPEPTIDE AND TRIPEPTIDE PERMEASE COMPND 8 YJDL,YJDL PEPTIDE TRANSPORTER; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DTPD_2, DTPC, DTPD_1, YJDL, AM464_14395, AT845_002896, SOURCE 5 AWP93_17895, BANRA_02817, BGZ_01664, BGZ_05066, BJI68_16865, SOURCE 6 BJJ90_24000, BO068_004094, BON64_05130, BON69_04615, BON71_15930, SOURCE 7 BON73_07300, BON74_00740, BON75_25330, BON77_18065, BON80_13570, SOURCE 8 BON89_26025, BON93_12630, BON97_19640, BVCMSF30A_02788, SOURCE 9 BVCMSHHP019_00793, BVCMSHHP056_00023, BVCMSKKP061_00271, SOURCE 10 C2U48_11920, C3F40_14675, C5N07_06940, C5Y87_09615, CA593_05175, SOURCE 11 CG831_003409, CIG67_08950, COD53_12960, CWS33_03315, D0X26_12710, SOURCE 12 D9D77_08965, DAH17_08915, DAH18_16490, DAH34_18055, DAH35_18055, SOURCE 13 DAH36_09805, DAH37_06440, DEN87_12425, DEO12_13910, DEO20_13520, SOURCE 14 DXT71_14295, DXT73_07155, E0I42_01290, E2119_15085, E2121_02870, SOURCE 15 E2122_03065, E2131_09650, E2135_09870, E4K51_08850, E5M02_11420, SOURCE 16 E5P26_01815, E5P27_12215, E5P28_03135, E5P29_19355, E5P31_11330, SOURCE 17 E5P32_03320, E5P33_11435, E5P35_07320, E5P36_20530, E5P40_16720, SOURCE 18 E5S34_00615, E5S35_05230, E5S36_08360, E5S37_06350, E5S42_15010, SOURCE 19 E5S43_14690, E5S45_06265, E5S51_06500, E5S54_12820, E5S57_19065, SOURCE 20 EC1094V2_4123, EC3234A_78C00250, EI021_09455, EIZ93_10840, SOURCE 21 EL79_4257, EL80_4164, ELT20_09370, ELT41_02450, ELV08_11600, SOURCE 22 ELY39_09460, ERS139208_00804, EYV17_05270, EYV18_19620, F2N31_14570, SOURCE 23 F9V24_13955, F9X20_06665, FDM60_18295, FOI11_014975, FOI11_20705, SOURCE 24 FQ007_15450, FQF29_19850, FV293_00630, G5632_13435, GF699_20045, SOURCE 25 GIB53_13155, GKF89_08690, GKG12_11445, GNZ05_19605, GP662_06300, SOURCE 26 GQF59_12650, GRW05_17855, GRW57_10485, GRW81_08175, H0O72_04690, SOURCE 27 HHH44_003360, HMV95_08810, HNC36_09415, HV109_21715, HVY77_23340, SOURCE 28 HX136_22920, I6H02_16470, IH768_20930, IH772_00050, J0541_004579, SOURCE 29 J4S20_000461, JFD_00784, JNP96_02330, NCTC10429_06294, SOURCE 30 NCTC11126_02220, NCTC11181_01802, NCTC13216_02261, NCTC8008_04125, SOURCE 31 NCTC9037_04624, NCTC9045_05367, NCTC9073_04059, PGD_03312, SOURCE 32 SAMEA3472067_03850, SAMEA3472080_00141, SAMEA3752557_02097, SOURCE 33 WP2S18E08_44130, WR15_07240; SOURCE 34 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 35 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE PROTEIN, PEPTIDE TRANSPORTER, PROTON COUPLED OLIGOPEPTIDE KEYWDS 2 TRANSPORTER, POT, MFS, DTPC., TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR M.KILLER,G.FINOCCHIO,E.PARDON,J.STEYAERT,C.LOEW REVDAT 2 10-AUG-22 7ZC2 1 JRNL REVDAT 1 06-JUL-22 7ZC2 0 JRNL AUTH M.KILLER,G.FINOCCHIO,H.D.T.MERTENS,D.I.SVERGUN,E.PARDON, JRNL AUTH 2 J.STEYAERT,C.LOW JRNL TITL CRYO-EM STRUCTURE OF AN ATYPICAL PROTON-COUPLED PEPTIDE JRNL TITL 2 TRANSPORTER: DI- AND TRIPEPTIDE PERMEASE C. JRNL REF FRONT MOL BIOSCI V. 9 17725 2022 JRNL REFN ESSN 2296-889X JRNL PMID 35898305 JRNL DOI 10.3389/FMOLB.2022.917725 REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, CTFFIND, CRYOSPARC 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) : 2.720 REMARK 3 NUMBER OF PARTICLES : 878428 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 7ZC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292121999. 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 : DIPEPTIDE AND TRIPEPTIDE REMARK 245 PERMEASE C (DTPC) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 6.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 24333 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) : 900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 7500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: 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 LEU A 472 REMARK 465 PHE A 473 REMARK 465 SER A 474 REMARK 465 THR A 475 REMARK 465 PRO A 476 REMARK 465 THR A 477 REMARK 465 ASN A 478 REMARK 465 MET A 479 REMARK 465 ILE A 480 REMARK 465 GLN A 481 REMARK 465 GLU A 482 REMARK 465 SER A 483 REMARK 465 ASN A 484 REMARK 465 ASP A 485 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 HH2 TRP A 278 OE2 GLU A 388 1.45 REMARK 500 CH2 TRP A 278 OE2 GLU A 388 2.16 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 LEU A 71 -59.88 -129.87 REMARK 500 PHE A 207 -137.81 52.28 REMARK 500 SER A 286 -85.55 -109.48 REMARK 500 ILE A 391 -73.95 -114.36 REMARK 500 THR A 400 2.58 -68.96 REMARK 500 MET A 404 13.87 58.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-14618 RELATED DB: EMDB REMARK 900 DIPEPTIDE AND TRIPEPTIDE PERMEASE C (DTPC) DBREF 7ZC2 A 1 485 UNP W8TWZ0 W8TWZ0_ECOLX 1 485 SEQRES 1 A 485 MET LYS THR PRO SER GLN PRO ARG ALA ILE TYR TYR ILE SEQRES 2 A 485 VAL ALA ILE GLN ILE TRP GLU TYR PHE SER PHE TYR GLY SEQRES 3 A 485 MET ARG ALA LEU LEU ILE LEU TYR LEU THR HIS GLN LEU SEQRES 4 A 485 GLY PHE ASP ASP ASN HIS ALA ILE SER LEU PHE SER ALA SEQRES 5 A 485 TYR ALA SER LEU VAL TYR VAL THR PRO ILE LEU GLY GLY SEQRES 6 A 485 TRP LEU ALA ASP ARG LEU LEU GLY ASN ARG THR ALA VAL SEQRES 7 A 485 ILE ALA GLY ALA LEU LEU MET THR LEU GLY HIS VAL VAL SEQRES 8 A 485 LEU GLY ILE ASP THR ASN SER THR PHE SER LEU TYR LEU SEQRES 9 A 485 ALA LEU ALA ILE ILE ILE CYS GLY TYR GLY LEU PHE LYS SEQRES 10 A 485 SER ASN ILE SER CYS LEU LEU GLY GLU LEU TYR ASP GLU SEQRES 11 A 485 ASN ASP HIS ARG ARG ASP GLY GLY PHE SER LEU LEU TYR SEQRES 12 A 485 ALA ALA GLY ASN ILE GLY SER ILE ALA ALA PRO ILE ALA SEQRES 13 A 485 CYS GLY LEU ALA ALA GLN TRP TYR GLY TRP HIS VAL GLY SEQRES 14 A 485 PHE ALA LEU ALA GLY GLY GLY MET PHE ILE GLY LEU LEU SEQRES 15 A 485 ILE PHE LEU SER GLY HIS ARG HIS PHE GLN SER THR ARG SEQRES 16 A 485 SER MET ASP LYS LYS ALA LEU THR SER VAL LYS PHE ALA SEQRES 17 A 485 LEU PRO VAL TRP SER TRP LEU VAL VAL MET LEU CYS LEU SEQRES 18 A 485 ALA PRO VAL PHE PHE THR LEU LEU LEU GLU ASN ASP TRP SEQRES 19 A 485 SER GLY TYR LEU LEU ALA ILE VAL CYS LEU ILE ALA ALA SEQRES 20 A 485 GLN ILE ILE ALA ARG MET MET ILE LYS PHE PRO GLU HIS SEQRES 21 A 485 ARG ARG ALA LEU TRP GLN ILE VAL LEU LEU MET PHE VAL SEQRES 22 A 485 GLY THR LEU PHE TRP VAL LEU ALA GLN GLN GLY GLY SER SEQRES 23 A 485 THR ILE SER LEU PHE ILE ASP ARG PHE VAL ASN ARG GLN SEQRES 24 A 485 ALA PHE ASN ILE GLU VAL PRO THR ALA LEU PHE GLN SER SEQRES 25 A 485 VAL ASN ALA ILE ALA VAL MET LEU ALA GLY VAL VAL LEU SEQRES 26 A 485 ALA TRP LEU ALA SER PRO GLU SER ARG GLY ASN SER THR SEQRES 27 A 485 LEU ARG VAL TRP LEU LYS PHE ALA PHE GLY LEU LEU LEU SEQRES 28 A 485 MET ALA CYS GLY PHE MET LEU LEU ALA PHE ASP ALA ARG SEQRES 29 A 485 HIS ALA ALA ALA ASP GLY GLN ALA SER MET GLY VAL MET SEQRES 30 A 485 ILE SER GLY LEU ALA LEU MET GLY PHE ALA GLU LEU PHE SEQRES 31 A 485 ILE ASP PRO VAL ALA ILE ALA GLN ILE THR ARG LEU LYS SEQRES 32 A 485 MET SER GLY VAL LEU THR GLY ILE TYR MET LEU ALA THR SEQRES 33 A 485 GLY ALA VAL ALA ASN TRP LEU ALA GLY VAL VAL ALA GLN SEQRES 34 A 485 GLN THR THR GLU SER GLN ILE SER GLY MET ALA ILE ALA SEQRES 35 A 485 ALA TYR GLN ARG PHE PHE SER GLN MET GLY GLU TRP THR SEQRES 36 A 485 LEU ALA CYS VAL ALA ILE ILE VAL VAL LEU ALA PHE ALA SEQRES 37 A 485 THR ARG PHE LEU PHE SER THR PRO THR ASN MET ILE GLN SEQRES 38 A 485 GLU SER ASN ASP HELIX 1 AA1 ARG A 8 GLN A 38 1 31 HELIX 2 AA2 ASP A 42 LEU A 71 1 30 HELIX 3 AA3 GLY A 73 ASP A 95 1 23 HELIX 4 AA4 SER A 98 LEU A 127 1 30 HELIX 5 AA5 ARG A 134 GLY A 165 1 32 HELIX 6 AA6 GLY A 165 GLY A 187 1 23 HELIX 7 AA7 HIS A 188 PHE A 191 5 4 HELIX 8 AA8 ASP A 198 THR A 203 1 6 HELIX 9 AA9 VAL A 211 ASN A 232 1 22 HELIX 10 AB1 TRP A 234 PHE A 257 1 24 HELIX 11 AB2 HIS A 260 GLN A 282 1 23 HELIX 12 AB3 SER A 286 VAL A 296 1 11 HELIX 13 AB4 PRO A 306 ALA A 308 5 3 HELIX 14 AB5 LEU A 309 LEU A 328 1 20 HELIX 15 AB6 ASN A 336 ALA A 366 1 31 HELIX 16 AB7 ALA A 367 ASP A 369 5 3 HELIX 17 AB8 SER A 373 GLU A 388 1 16 HELIX 18 AB9 ILE A 391 THR A 400 1 10 HELIX 19 AC1 MET A 404 GLN A 429 1 26 HELIX 20 AC2 GLN A 430 GLU A 433 5 4 HELIX 21 AC3 ALA A 440 THR A 469 1 30 SHEET 1 AA1 2 VAL A 205 LYS A 206 0 SHEET 2 AA1 2 LEU A 209 PRO A 210 -1 O LEU A 209 N LYS A 206 SHEET 1 AA2 2 GLN A 299 ALA A 300 0 SHEET 2 AA2 2 ILE A 303 GLU A 304 -1 O ILE A 303 N ALA A 300 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