HEADER PROTEIN TRANSPORT 04-MAY-20 6WU0 TITLE CRYOEM STRUCTURE OF BURKHOLDERIA PSEUDOMALLEI HOPANOID BIOSYNTHESIS- TITLE 2 ASSOCIATED RND TRANSPORTER HPNN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOPANOID BIOSYNTHESIS ASSOCIATED RND TRANSPORTER LIKE COMPND 3 PROTEIN HPNN; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI MSHR346; SOURCE 3 ORGANISM_TAXID: 536230; SOURCE 4 GENE: HPNN, GBP346_B2639; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRYOEM STRUCTURE, HOPANOID TRANSPORTER HPNN, PROTEIN TRANSPORT EXPDTA ELECTRON MICROSCOPY AUTHOR M.LYU,E.W.YU REVDAT 2 06-MAR-24 6WU0 1 REMARK REVDAT 1 03-FEB-21 6WU0 0 JRNL AUTH C.C.SU,M.LYU,C.E.MORGAN,J.R.BOLLA,C.V.ROBINSON,E.W.YU JRNL TITL A 'BUILD AND RETRIEVE' METHODOLOGY TO SIMULTANEOUSLY SOLVE JRNL TITL 2 CRYO-EM STRUCTURES OF MEMBRANE PROTEINS. JRNL REF NAT.METHODS V. 18 69 2021 JRNL REFN ESSN 1548-7105 JRNL PMID 33408407 JRNL DOI 10.1038/S41592-020-01021-2 REMARK 2 REMARK 2 RESOLUTION. 3.59 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) : 3.590 REMARK 3 NUMBER OF PARTICLES : 63910 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 6WU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000249002. 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 : HOPANOID TRANSPORTER HPNN 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 : 7.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 5000.00 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 PRO B 432 REMARK 465 GLY B 433 REMARK 465 GLU B 434 REMARK 465 ARG B 435 REMARK 465 LYS B 436 REMARK 465 PRO B 437 REMARK 465 GLY B 861 REMARK 465 LYS B 862 REMARK 465 PRO B 863 REMARK 465 ARG B 864 REMARK 465 THR B 865 REMARK 465 LYS B 866 REMARK 465 ARG B 867 REMARK 465 VAL B 868 REMARK 465 THR B 869 REMARK 465 ASN B 870 REMARK 465 GLN B 871 REMARK 465 SER B 872 REMARK 465 GLN B 873 REMARK 465 GLY B 874 REMARK 465 ILE B 875 REMARK 465 ASP B 876 REMARK 465 GLU B 877 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 PRO B 17 -167.64 -72.93 REMARK 500 PHE B 124 30.49 -96.16 REMARK 500 LEU B 205 -61.56 -94.76 REMARK 500 ASN B 226 65.89 60.03 REMARK 500 LYS B 231 1.67 -67.99 REMARK 500 SER B 298 142.81 -170.98 REMARK 500 ASN B 328 26.59 49.32 REMARK 500 MET B 329 -6.38 67.97 REMARK 500 ARG B 359 -60.62 -95.02 REMARK 500 PHE B 440 71.57 52.39 REMARK 500 HIS B 474 55.93 -93.09 REMARK 500 ASP B 486 74.22 54.21 REMARK 500 PRO B 530 4.20 -66.28 REMARK 500 PRO B 573 173.77 -59.75 REMARK 500 ALA B 614 37.12 -98.54 REMARK 500 GLN B 644 72.77 -117.87 REMARK 500 ASP B 681 154.55 -48.74 REMARK 500 PHE B 855 53.69 -91.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-21901 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF BURKHOLDERIA PSEUDOMALLEI HOPANOID BIOSYNTHESIS- REMARK 900 ASSOCIATED RND TRANSPORTER HPNN DBREF 6WU0 B 1 877 UNP C4I4K0 C4I4K0_BURPE 96 972 SEQADV 6WU0 VAL B 517 UNP C4I4K0 ALA 612 CONFLICT SEQADV 6WU0 GLY B 559 UNP C4I4K0 GLU 654 CONFLICT SEQADV 6WU0 LEU B 646 UNP C4I4K0 SER 741 CONFLICT SEQRES 1 B 877 MET LEU THR SER VAL LEU VAL ARG LEU VAL ALA TRP SER SEQRES 2 B 877 VAL ARG ARG PRO ILE TRP VAL VAL VAL LEU SER LEU VAL SEQRES 3 B 877 ILE ALA ALA LEU SER SER VAL TYR VAL ALA HIS HIS PHE SEQRES 4 B 877 LYS ILE ASN THR ASP ILE SER LYS LEU VAL GLU ASN ASP SEQRES 5 B 877 PRO LYS TRP ALA ALA LEU GLY ARG ALA ILE ASP ASP ALA SEQRES 6 B 877 PHE PRO GLN ARG ASN GLN THR ILE LEU ALA VAL VAL GLU SEQRES 7 B 877 ALA PRO ALA PRO GLU PHE ALA GLY ALA ALA ALA ASP ALA SEQRES 8 B 877 LEU ALA GLU GLY LEU ARG ARG GLU THR GLU ALA GLY ARG SEQRES 9 B 877 ILE GLY GLN VAL SER GLU PRO ALA GLY GLY PRO LEU PHE SEQRES 10 B 877 GLU HIS ASP GLY LEU LEU PHE LEU PRO GLU GLN ASP VAL SEQRES 11 B 877 ALA THR THR THR ALA GLN LEU ALA SER ALA ARG PRO LEU SEQRES 12 B 877 ILE ASN VAL LEU ALA LYS ASP PRO SER ILE ALA GLY LEU SEQRES 13 B 877 ALA THR THR LEU SER THR THR LEU GLY VAL PRO LEU GLN SEQRES 14 B 877 SER GLY GLN VAL LYS LEU SER GLY MET ALA LYS LEU LEU SEQRES 15 B 877 SER ARG SER ALA ALA THR VAL ASP ASP VAL LEU ALA GLY SEQRES 16 B 877 LYS PRO ALA ALA PHE SER TRP ARG ALA LEU VAL ASP ALA SEQRES 17 B 877 ASP ALA ALA ARG GLU PRO ALA ARG ALA PHE VAL THR VAL SEQRES 18 B 877 GLN PRO VAL VAL ASN TYR GLY ALA LEU LYS ALA GLY GLU SEQRES 19 B 877 GLN ALA SER ARG THR ILE ARG ALA THR ALA GLN ALA LEU SEQRES 20 B 877 LYS LEU ASP GLU ARG PHE GLY ALA ALA VAL ARG LEU THR SEQRES 21 B 877 GLY GLU GLN PRO LEU ALA ASP GLU GLU PHE ALA SER VAL SEQRES 22 B 877 GLN ASP GLY ALA LEU VAL ASN GLY ILE ALA THR LEU ALA SEQRES 23 B 877 ILE VAL LEU VAL ILE LEU TRP ILE ALA LEU ARG SER LYS SEQRES 24 B 877 ARG MET ILE ALA SER VAL PHE VAL THR LEU PHE VAL GLY SEQRES 25 B 877 LEU VAL VAL THR ALA ALA LEU GLY LEU MET MET VAL GLY SEQRES 26 B 877 SER LEU ASN MET ILE SER VAL ALA PHE MET VAL LEU PHE SEQRES 27 B 877 VAL GLY LEU GLY VAL ASP PHE ALA ILE GLN TYR GLY VAL SEQRES 28 B 877 LYS TYR ARG GLU GLU ARG HIS ARG ASP PRO ASN LEU ASP SEQRES 29 B 877 HIS ALA LEU VAL GLY ALA ALA HIS ALA MET GLY MET PRO SEQRES 30 B 877 LEU THR LEU ALA THR ALA ALA VAL ALA ALA SER PHE PHE SEQRES 31 B 877 SER PHE LEU PRO THR ALA TYR ARG GLY VAL SER GLU LEU SEQRES 32 B 877 GLY LEU ILE ALA GLY VAL GLY MET PHE VAL ALA LEU PHE SEQRES 33 B 877 THR THR LEU THR LEU LEU PRO ALA LEU LEU LYS LEU LEU SEQRES 34 B 877 ALA PRO PRO GLY GLU ARG LYS PRO PRO GLY PHE PRO ARG SEQRES 35 B 877 LEU ALA PRO VAL ASP ASP TYR LEU ASP HIS HIS ARG LYS SEQRES 36 B 877 PRO ILE LEU ILE GLY THR LEU ALA VAL VAL ILE GLY ALA SEQRES 37 B 877 LEU PRO LEU LEU ALA HIS LEU ARG PHE ASP PHE ASN PRO SEQRES 38 B 877 LEU HIS LEU LYS ASP PRO ARG SER GLU SER MET ALA THR SEQRES 39 B 877 LEU LEU ALA LEU LYS ASP SER PRO GLU ALA SER VAL ASN SEQRES 40 B 877 ASP VAL SER LEU LEU ALA PRO SER LEU VAL ALA ALA ASN SEQRES 41 B 877 ALA ALA ALA GLN ARG LEU GLY ALA LEU PRO GLU VAL GLY SEQRES 42 B 877 ARG THR THR THR LEU SER THR PHE ILE PRO ASP ALA GLN SEQRES 43 B 877 PRO GLN LYS LEU ALA THR ILE ALA ALA ALA ALA ARG GLY SEQRES 44 B 877 LEU LEU PRO ALA LEU THR GLN PRO ALA ALA ALA PRO VAL SEQRES 45 B 877 PRO ASP ALA GLN ARG VAL ALA ALA LEU LYS ARG ALA SER SEQRES 46 B 877 ASN LEU LEU GLU TYR ALA SER GLU ASP TYR PRO GLY PRO SEQRES 47 B 877 GLY ALA ALA ALA ALA LYS HIS LEU SER GLU SER LEU ALA SEQRES 48 B 877 LYS LEU ALA ALA ALA ASP ALA ALA THR ARG GLU ARG ALA SEQRES 49 B 877 GLU HIS ALA PHE SER VAL PRO LEU LYS ILE ALA LEU ASN SEQRES 50 B 877 GLN LEU ALA MET LEU LEU GLN PRO LEU GLU ILE THR ARG SEQRES 51 B 877 GLU ASN LEU PRO PRO GLN ILE VAL ARG ASP TRP ILE ALA SEQRES 52 B 877 PRO ASP GLY ARG ALA LEU VAL GLN ILE SER PRO LYS VAL SEQRES 53 B 877 VAL LYS GLY ALA ASP PRO GLY ASP ASP ALA MET LEU ARG SEQRES 54 B 877 ARG PHE ALA LYS ALA VAL LYS ALA ALA GLU PRO GLY ALA SEQRES 55 B 877 ILE GLY GLY PRO ILE SER ILE LEU HIS SER ALA ASP THR SEQRES 56 B 877 ILE ILE ARG ALA PHE LEU GLN ALA ALA ALA LEU SER VAL SEQRES 57 B 877 VAL SER ILE THR VAL LEU LEU TRP ILE THR LEU ARG ARG SEQRES 58 B 877 PHE GLY ASP VAL LEU ARG THR LEU VAL PRO LEU LEU VAL SEQRES 59 B 877 SER GLY VAL VAL THR LEU GLU LEU CYS VAL LEU LEU GLY SEQRES 60 B 877 MET PRO LEU ASN PHE ALA ASN ILE ILE ALA LEU PRO LEU SEQRES 61 B 877 MET LEU GLY VAL GLY VAL ALA PHE LYS VAL TYR PHE VAL SEQRES 62 B 877 MET ALA TRP ARG ALA GLY GLN THR GLY LEU LEU GLN SER SEQRES 63 B 877 SER LEU THR HIS ALA VAL LEU PHE SER ALA ALA THR THR SEQRES 64 B 877 ALA THR ALA PHE GLY SER LEU TRP LEU SER HIS HIS PRO SEQRES 65 B 877 GLY THR ALA SER MET GLY ARG LEU LEU ALA LEU ALA LEU SEQRES 66 B 877 SER CYS THR LEU ILE GLY ALA VAL VAL PHE GLN PRO VAL SEQRES 67 B 877 LEU MET GLY LYS PRO ARG THR LYS ARG VAL THR ASN GLN SEQRES 68 B 877 SER GLN GLY ILE ASP GLU HELIX 1 AA1 MET B 1 ARG B 15 1 15 HELIX 2 AA2 ILE B 18 HIS B 38 1 21 HELIX 3 AA3 ASP B 52 PHE B 66 1 15 HELIX 4 AA4 PRO B 67 ASN B 70 5 4 HELIX 5 AA5 ALA B 81 ALA B 102 1 22 HELIX 6 AA6 GLY B 114 ASP B 120 1 7 HELIX 7 AA7 PRO B 126 ALA B 140 1 15 HELIX 8 AA8 ALA B 140 LYS B 149 1 10 HELIX 9 AA9 SER B 152 GLY B 171 1 20 HELIX 10 AB1 LYS B 174 GLY B 177 5 4 HELIX 11 AB2 MET B 178 ALA B 194 1 17 HELIX 12 AB3 GLY B 233 LEU B 247 1 15 HELIX 13 AB4 LYS B 248 PHE B 253 1 6 HELIX 14 AB5 GLY B 261 GLY B 276 1 16 HELIX 15 AB6 ALA B 277 LEU B 296 1 20 HELIX 16 AB7 SER B 298 VAL B 324 1 27 HELIX 17 AB8 ILE B 330 VAL B 332 5 3 HELIX 18 AB9 ALA B 333 GLY B 342 1 10 HELIX 19 AC1 GLY B 342 ASP B 360 1 19 HELIX 20 AC2 LEU B 363 MET B 374 1 12 HELIX 21 AC3 GLY B 375 SER B 391 1 17 HELIX 22 AC4 TYR B 397 LEU B 429 1 33 HELIX 23 AC5 LEU B 443 LEU B 450 1 8 HELIX 24 AC6 PRO B 456 GLY B 467 1 12 HELIX 25 AC7 ALA B 468 ALA B 473 5 6 HELIX 26 AC8 ASN B 480 LYS B 485 5 6 HELIX 27 AC9 SER B 489 LEU B 498 1 10 HELIX 28 AD1 SER B 515 ALA B 528 1 14 HELIX 29 AD2 LEU B 538 ILE B 542 5 5 HELIX 30 AD3 ALA B 545 LEU B 561 1 17 HELIX 31 AD4 PRO B 562 LEU B 564 5 3 HELIX 32 AD5 PRO B 573 TYR B 595 1 23 HELIX 33 AD6 GLY B 599 ALA B 614 1 16 HELIX 34 AD7 ALA B 618 GLN B 644 1 27 HELIX 35 AD8 THR B 649 LEU B 653 5 5 HELIX 36 AD9 PRO B 654 ILE B 662 1 9 HELIX 37 AE1 ASP B 684 GLU B 699 1 16 HELIX 38 AE2 GLY B 705 SER B 708 5 4 HELIX 39 AE3 ILE B 709 LEU B 739 1 31 HELIX 40 AE4 ARG B 741 GLY B 767 1 27 HELIX 41 AE5 ILE B 776 TRP B 796 1 21 HELIX 42 AE6 ARG B 797 GLY B 799 5 3 HELIX 43 AE7 THR B 809 LEU B 828 1 20 HELIX 44 AE8 HIS B 831 VAL B 854 1 24 HELIX 45 AE9 PHE B 855 LEU B 859 5 5 SHEET 1 AA1 4 VAL B 108 SER B 109 0 SHEET 2 AA1 4 ALA B 215 VAL B 221 -1 O THR B 220 N SER B 109 SHEET 3 AA1 4 ILE B 73 ALA B 79 -1 N ALA B 75 O VAL B 219 SHEET 4 AA1 4 ALA B 256 THR B 260 -1 O ARG B 258 N VAL B 76 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