HEADER TRANSPORT PROTEIN 27-JAN-26 22XP TITLE STRUCTURE OF A PERMEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PTS SYSTEM MANNITOL-SPECIFIC EIICBA COMPONENT; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: EIICBA-MTL,EII-MTL; COMPND 5 EC: 2.7.1.197; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: MTLA, B3599, JW3573; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, NUTRIENT, MEMBRANE, DRUG TARGET, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Z.JINRU,Z.JINRU REVDAT 1 04-NOV-26 22XP 0 JRNL AUTH Z.JINRU,Z.JINRU JRNL TITL STRUCTURE OF A PERMEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 297409 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 22XP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1300062913. 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 : COMPLEX OF PERMEASE A REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 3000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 505 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 506 CG CD CE NZ REMARK 470 THR A 509 OG1 CG2 REMARK 470 GLU A 511 CG CD OE1 OE2 REMARK 470 GLU A 512 CG CD OE1 OE2 REMARK 470 ARG A 515 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 523 CG CD CE NZ REMARK 470 VAL A 527 CG1 CG2 REMARK 470 GLU A 528 CG CD OE1 OE2 REMARK 470 VAL A 557 CG1 CG2 REMARK 470 LYS A 560 CG CD CE NZ REMARK 470 ARG A 562 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 564 CG CD1 CD2 REMARK 470 LYS A 565 CG CD CE NZ REMARK 470 GLN A 572 CG CD OE1 NE2 REMARK 470 TYR A 573 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 575 CG CD OE1 OE2 REMARK 470 VAL A 577 CG1 CG2 REMARK 470 ARG A 578 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 579 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 581 CG CD OE1 OE2 REMARK 470 GLU A 582 CG CD OE1 OE2 REMARK 470 GLU A 583 CG CD OE1 OE2 REMARK 470 ASP A 584 CG OD1 OD2 REMARK 470 ASP A 585 CG OD1 OD2 REMARK 470 ILE A 586 CG1 CG2 CD1 REMARK 470 ARG A 588 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 596 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 597 CG OD1 ND2 REMARK 470 ASN A 598 CG OD1 ND2 REMARK 470 HIS A 600 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 613 CG OD1 OD2 REMARK 470 GLU A 614 CG CD OE1 OE2 REMARK 470 THR A 624 OG1 CG2 REMARK 470 SER A 625 OG REMARK 470 VAL A 626 CG1 CG2 REMARK 470 ASP A 627 CG OD1 OD2 REMARK 470 GLU A 628 CG CD OE1 OE2 REMARK 470 VAL A 629 CG1 CG2 REMARK 470 LEU A 630 CG CD1 CD2 REMARK 470 GLU A 631 CG CD OE1 OE2 REMARK 470 LEU A 632 CG CD1 CD2 REMARK 470 LEU A 633 CG CD1 CD2 REMARK 470 GLU B 499 CG CD OE1 OE2 REMARK 470 ARG B 505 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 506 CG CD CE NZ REMARK 470 THR B 509 OG1 CG2 REMARK 470 GLU B 511 CG CD OE1 OE2 REMARK 470 GLU B 512 CG CD OE1 OE2 REMARK 470 ARG B 515 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 523 CG CD CE NZ REMARK 470 VAL B 527 CG1 CG2 REMARK 470 GLU B 528 CG CD OE1 OE2 REMARK 470 VAL B 557 CG1 CG2 REMARK 470 GLU B 558 CG CD OE1 OE2 REMARK 470 LYS B 560 CG CD CE NZ REMARK 470 ASP B 561 CG OD1 OD2 REMARK 470 ARG B 562 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 564 CG CD1 CD2 REMARK 470 LYS B 565 CG CD CE NZ REMARK 470 GLN B 572 CG CD OE1 NE2 REMARK 470 TYR B 573 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 575 CG CD OE1 OE2 REMARK 470 VAL B 577 CG1 CG2 REMARK 470 ARG B 578 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 579 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 581 CG CD OE1 OE2 REMARK 470 GLU B 582 CG CD OE1 OE2 REMARK 470 GLU B 583 CG CD OE1 OE2 REMARK 470 ASP B 584 CG OD1 OD2 REMARK 470 ASP B 585 CG OD1 OD2 REMARK 470 ILE B 586 CG1 CG2 CD1 REMARK 470 ARG B 588 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 596 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 597 CG OD1 ND2 REMARK 470 ASN B 598 CG OD1 ND2 REMARK 470 HIS B 600 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 613 CG OD1 OD2 REMARK 470 GLU B 614 CG CD OE1 OE2 REMARK 470 THR B 624 OG1 CG2 REMARK 470 SER B 625 OG REMARK 470 VAL B 626 CG1 CG2 REMARK 470 ASP B 627 CG OD1 OD2 REMARK 470 GLU B 628 CG CD OE1 OE2 REMARK 470 VAL B 629 CG1 CG2 REMARK 470 LEU B 630 CG CD1 CD2 REMARK 470 GLU B 631 CG CD OE1 OE2 REMARK 470 LEU B 632 CG CD1 CD2 REMARK 470 LEU B 633 CG CD1 CD2 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 374 32.91 -98.18 REMARK 500 SER A 485 -3.99 69.67 REMARK 500 SER A 489 -137.31 51.86 REMARK 500 GLU A 499 49.54 -89.57 REMARK 500 ASN A 500 -0.43 -140.89 REMARK 500 LEU A 503 -123.34 57.31 REMARK 500 GLU A 530 -4.32 69.25 REMARK 500 THR A 542 -113.56 54.01 REMARK 500 GLU A 581 -123.34 52.08 REMARK 500 ASN A 597 -144.87 58.05 REMARK 500 HIS A 600 5.39 -69.97 REMARK 500 THR A 623 178.53 56.90 REMARK 500 ASN B 474 -7.70 71.43 REMARK 500 SER B 489 -143.15 46.44 REMARK 500 LEU B 503 -121.01 57.00 REMARK 500 GLU B 528 158.04 68.18 REMARK 500 GLU B 530 -0.06 74.52 REMARK 500 LYS B 565 -169.24 -161.92 REMARK 500 GLU B 581 -150.14 59.14 REMARK 500 ASN B 597 -145.13 58.31 REMARK 500 HIS B 600 7.83 -69.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-68757 RELATED DB: EMDB REMARK 900 STRUCTURE OF A PERMEASE DBREF 22XP A 372 635 UNP P00550 PTM3C_ECOLI 372 635 DBREF 22XP B 372 635 UNP P00550 PTM3C_ECOLI 372 635 SEQRES 1 A 264 ASN ASP LEU SER HIS VAL ARG LYS ILE ILE VAL ALA CYS SEQRES 2 A 264 ASP ALA GLY MET GLY SER SER ALA MET GLY ALA GLY VAL SEQRES 3 A 264 LEU ARG LYS LYS ILE GLN ASP ALA GLY LEU SER GLN ILE SEQRES 4 A 264 SER VAL THR ASN SER ALA ILE ASN ASN LEU PRO PRO ASP SEQRES 5 A 264 VAL ASP LEU VAL ILE THR HIS ARG ASP LEU THR GLU ARG SEQRES 6 A 264 ALA MET ARG GLN VAL PRO GLN ALA GLN HIS ILE SER LEU SEQRES 7 A 264 THR ASN PHE LEU ASP SER GLY LEU TYR THR SER LEU THR SEQRES 8 A 264 GLU ARG LEU VAL ALA ALA GLN ARG HIS THR ALA ASN GLU SEQRES 9 A 264 GLU LYS VAL LYS ASP SER LEU LYS ASP SER PHE ASP ASP SEQRES 10 A 264 SER SER ALA ASN LEU PHE LYS LEU GLY ALA GLU ASN ILE SEQRES 11 A 264 PHE LEU GLY ARG LYS ALA ALA THR LYS GLU GLU ALA ILE SEQRES 12 A 264 ARG PHE ALA GLY GLU GLN LEU VAL LYS GLY GLY TYR VAL SEQRES 13 A 264 GLU PRO GLU TYR VAL GLN ALA MET LEU ASP ARG GLU LYS SEQRES 14 A 264 LEU THR PRO THR TYR LEU GLY GLU SER ILE ALA VAL PRO SEQRES 15 A 264 HIS GLY THR VAL GLU ALA LYS ASP ARG VAL LEU LYS THR SEQRES 16 A 264 GLY VAL VAL PHE CYS GLN TYR PRO GLU GLY VAL ARG PHE SEQRES 17 A 264 GLY GLU GLU GLU ASP ASP ILE ALA ARG LEU VAL ILE GLY SEQRES 18 A 264 ILE ALA ALA ARG ASN ASN GLU HIS ILE GLN VAL ILE THR SEQRES 19 A 264 SER LEU THR ASN ALA LEU ASP ASP GLU SER VAL ILE GLU SEQRES 20 A 264 ARG LEU ALA HIS THR THR SER VAL ASP GLU VAL LEU GLU SEQRES 21 A 264 LEU LEU ALA GLY SEQRES 1 B 264 ASN ASP LEU SER HIS VAL ARG LYS ILE ILE VAL ALA CYS SEQRES 2 B 264 ASP ALA GLY MET GLY SER SER ALA MET GLY ALA GLY VAL SEQRES 3 B 264 LEU ARG LYS LYS ILE GLN ASP ALA GLY LEU SER GLN ILE SEQRES 4 B 264 SER VAL THR ASN SER ALA ILE ASN ASN LEU PRO PRO ASP SEQRES 5 B 264 VAL ASP LEU VAL ILE THR HIS ARG ASP LEU THR GLU ARG SEQRES 6 B 264 ALA MET ARG GLN VAL PRO GLN ALA GLN HIS ILE SER LEU SEQRES 7 B 264 THR ASN PHE LEU ASP SER GLY LEU TYR THR SER LEU THR SEQRES 8 B 264 GLU ARG LEU VAL ALA ALA GLN ARG HIS THR ALA ASN GLU SEQRES 9 B 264 GLU LYS VAL LYS ASP SER LEU LYS ASP SER PHE ASP ASP SEQRES 10 B 264 SER SER ALA ASN LEU PHE LYS LEU GLY ALA GLU ASN ILE SEQRES 11 B 264 PHE LEU GLY ARG LYS ALA ALA THR LYS GLU GLU ALA ILE SEQRES 12 B 264 ARG PHE ALA GLY GLU GLN LEU VAL LYS GLY GLY TYR VAL SEQRES 13 B 264 GLU PRO GLU TYR VAL GLN ALA MET LEU ASP ARG GLU LYS SEQRES 14 B 264 LEU THR PRO THR TYR LEU GLY GLU SER ILE ALA VAL PRO SEQRES 15 B 264 HIS GLY THR VAL GLU ALA LYS ASP ARG VAL LEU LYS THR SEQRES 16 B 264 GLY VAL VAL PHE CYS GLN TYR PRO GLU GLY VAL ARG PHE SEQRES 17 B 264 GLY GLU GLU GLU ASP ASP ILE ALA ARG LEU VAL ILE GLY SEQRES 18 B 264 ILE ALA ALA ARG ASN ASN GLU HIS ILE GLN VAL ILE THR SEQRES 19 B 264 SER LEU THR ASN ALA LEU ASP ASP GLU SER VAL ILE GLU SEQRES 20 B 264 ARG LEU ALA HIS THR THR SER VAL ASP GLU VAL LEU GLU SEQRES 21 B 264 LEU LEU ALA GLY HELIX 1 AA1 GLY A 389 GLY A 406 1 18 HELIX 2 AA2 LEU A 433 VAL A 441 1 9 HELIX 3 AA3 ASP A 454 LEU A 482 1 29 HELIX 4 AA4 THR A 509 LYS A 523 1 15 HELIX 5 AA5 TYR A 531 ASP A 537 1 7 HELIX 6 AA6 VAL A 557 ARG A 562 5 6 HELIX 7 AA7 HIS A 600 ASP A 613 1 14 HELIX 8 AA8 ASP A 613 HIS A 622 1 10 HELIX 9 AA9 SER A 625 ALA A 634 1 10 HELIX 10 AB1 GLY B 389 GLY B 406 1 18 HELIX 11 AB2 LEU B 433 VAL B 441 1 9 HELIX 12 AB3 ASP B 454 ALA B 473 1 20 HELIX 13 AB4 ASN B 474 SER B 481 1 8 HELIX 14 AB5 THR B 509 GLY B 524 1 16 HELIX 15 AB6 GLU B 530 ASP B 537 1 8 HELIX 16 AB7 VAL B 557 ARG B 562 5 6 HELIX 17 AB8 HIS B 600 ASP B 613 1 14 HELIX 18 AB9 GLU B 614 HIS B 622 1 9 HELIX 19 AC1 SER B 625 ALA B 634 1 10 SHEET 1 AA1 4 SER A 411 ALA A 416 0 SHEET 2 AA1 4 LYS A 379 CYS A 384 1 N ILE A 380 O SER A 411 SHEET 3 AA1 4 LEU A 426 THR A 429 1 O ILE A 428 N ILE A 381 SHEET 4 AA1 4 GLN A 445 SER A 448 1 O GLN A 445 N VAL A 427 SHEET 1 AA2 3 ILE A 550 ALA A 551 0 SHEET 2 AA2 3 ALA A 587 ALA A 594 1 O LEU A 589 N ALA A 551 SHEET 3 AA2 3 GLY A 567 VAL A 577 -1 N TYR A 573 O ARG A 588 SHEET 1 AA3 4 SER B 411 ALA B 416 0 SHEET 2 AA3 4 LYS B 379 CYS B 384 1 N ILE B 380 O SER B 411 SHEET 3 AA3 4 LEU B 426 THR B 429 1 O ILE B 428 N ILE B 381 SHEET 4 AA3 4 GLN B 445 SER B 448 1 O GLN B 445 N VAL B 427 SHEET 1 AA4 3 ILE B 550 ALA B 551 0 SHEET 2 AA4 3 ASP B 585 ALA B 594 1 O LEU B 589 N ALA B 551 SHEET 3 AA4 3 GLY B 567 GLY B 580 -1 N TYR B 573 O ARG B 588 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 MASTER 230 0 0 19 14 0 0 6 3711 2 0 42 END