HEADER TRANSPORT PROTEIN 13-AUG-23 8TTG TITLE NORA SINGLE MUTANT - E222Q AT PH 7.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: QUINOLONE RESISTANCE PROTEIN NORA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FABDA1 CDRH3 LOOP; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: NORA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E222Q NORA, EFFLUX PUMP, MRSA, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.P.LI,Y.LI,A.KOIDE,H.H.KUANG,V.J.TORRES,S.KOIDE,D.N.WANG, AUTHOR 2 N.J.TRAASETH REVDAT 2 03-JUL-24 8TTG 1 JRNL REVDAT 1 29-MAY-24 8TTG 0 JRNL AUTH J.LI,Y.LI,A.KOIDE,H.KUANG,V.J.TORRES,S.KOIDE,D.N.WANG, JRNL AUTH 2 N.J.TRAASETH JRNL TITL PROTON-COUPLED TRANSPORT MECHANISM OF THE EFFLUX PUMP NORA. JRNL REF NAT COMMUN V. 15 4494 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38802368 JRNL DOI 10.1038/S41467-024-48759-3 REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 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) : 3.350 REMARK 3 NUMBER OF PARTICLES : 246742 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 8TTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000276435. 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 : E222Q-NORA:FABDA1 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) : 1000.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5296.00 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 LYS A 181 REMARK 465 LYS A 182 REMARK 465 SER A 183 REMARK 465 THR A 184 REMARK 465 THR A 185 REMARK 465 SER A 186 REMARK 465 GLY A 187 REMARK 465 PHE A 188 REMARK 465 GLN A 189 REMARK 465 LYS A 190 REMARK 465 LEU A 191 REMARK 465 GLU A 192 REMARK 465 ASN A 387 REMARK 465 MET A 388 REMARK 465 GLU A 389 REMARK 465 ASN A 390 REMARK 465 LEU A 391 REMARK 465 TYR A 392 REMARK 465 PHE A 393 REMARK 465 GLN A 394 REMARK 465 GLY A 395 REMARK 465 LYS A 396 REMARK 465 LEU A 397 REMARK 465 GLY A 398 REMARK 465 PRO A 399 REMARK 465 GLU A 400 REMARK 465 GLN A 401 REMARK 465 LYS A 402 REMARK 465 LEU A 403 REMARK 465 ILE A 404 REMARK 465 SER A 405 REMARK 465 GLU A 406 REMARK 465 GLU A 407 REMARK 465 ASP A 408 REMARK 465 LEU A 409 REMARK 465 ASN A 410 REMARK 465 SER A 411 REMARK 465 ALA A 412 REMARK 465 VAL A 413 REMARK 465 ASP A 414 REMARK 465 HIS A 415 REMARK 465 HIS A 416 REMARK 465 HIS A 417 REMARK 465 HIS A 418 REMARK 465 HIS A 419 REMARK 465 HIS A 420 REMARK 465 HIS A 421 REMARK 465 HIS A 422 REMARK 465 HIS A 423 REMARK 465 HIS A 424 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 O GLY A 145 OG SER A 241 2.11 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 SER A 138 -1.11 -57.51 REMARK 500 TRP A 201 -2.59 68.13 REMARK 500 PHE C 134 1.35 59.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41607 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-41605 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-41606 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-41608 RELATED DB: EMDB DBREF 8TTG A 1 388 UNP Q53459 Q53459_STAAU 1 388 DBREF 8TTG C 126 140 PDB 8TTG 8TTG 126 140 SEQADV 8TTG GLN A 222 UNP Q53459 GLU 222 ENGINEERED MUTATION SEQADV 8TTG GLU A 389 UNP Q53459 EXPRESSION TAG SEQADV 8TTG ASN A 390 UNP Q53459 EXPRESSION TAG SEQADV 8TTG LEU A 391 UNP Q53459 EXPRESSION TAG SEQADV 8TTG TYR A 392 UNP Q53459 EXPRESSION TAG SEQADV 8TTG PHE A 393 UNP Q53459 EXPRESSION TAG SEQADV 8TTG GLN A 394 UNP Q53459 EXPRESSION TAG SEQADV 8TTG GLY A 395 UNP Q53459 EXPRESSION TAG SEQADV 8TTG LYS A 396 UNP Q53459 EXPRESSION TAG SEQADV 8TTG LEU A 397 UNP Q53459 EXPRESSION TAG SEQADV 8TTG GLY A 398 UNP Q53459 EXPRESSION TAG SEQADV 8TTG PRO A 399 UNP Q53459 EXPRESSION TAG SEQADV 8TTG GLU A 400 UNP Q53459 EXPRESSION TAG SEQADV 8TTG GLN A 401 UNP Q53459 EXPRESSION TAG SEQADV 8TTG LYS A 402 UNP Q53459 EXPRESSION TAG SEQADV 8TTG LEU A 403 UNP Q53459 EXPRESSION TAG SEQADV 8TTG ILE A 404 UNP Q53459 EXPRESSION TAG SEQADV 8TTG SER A 405 UNP Q53459 EXPRESSION TAG SEQADV 8TTG GLU A 406 UNP Q53459 EXPRESSION TAG SEQADV 8TTG GLU A 407 UNP Q53459 EXPRESSION TAG SEQADV 8TTG ASP A 408 UNP Q53459 EXPRESSION TAG SEQADV 8TTG LEU A 409 UNP Q53459 EXPRESSION TAG SEQADV 8TTG ASN A 410 UNP Q53459 EXPRESSION TAG SEQADV 8TTG SER A 411 UNP Q53459 EXPRESSION TAG SEQADV 8TTG ALA A 412 UNP Q53459 EXPRESSION TAG SEQADV 8TTG VAL A 413 UNP Q53459 EXPRESSION TAG SEQADV 8TTG ASP A 414 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 415 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 416 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 417 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 418 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 419 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 420 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 421 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 422 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 423 UNP Q53459 EXPRESSION TAG SEQADV 8TTG HIS A 424 UNP Q53459 EXPRESSION TAG SEQRES 1 A 424 MET ASN LYS GLN ILE PHE VAL LEU TYR PHE ASN ILE PHE SEQRES 2 A 424 LEU ILE PHE LEU GLY ILE GLY LEU VAL ILE PRO VAL LEU SEQRES 3 A 424 PRO VAL TYR LEU LYS ASP LEU GLY LEU THR GLY SER ASP SEQRES 4 A 424 LEU GLY LEU LEU VAL ALA ALA PHE ALA LEU SER GLN MET SEQRES 5 A 424 ILE ILE SER PRO PHE GLY GLY THR LEU ALA ASP LYS LEU SEQRES 6 A 424 GLY LYS LYS LEU ILE ILE CYS ILE GLY LEU ILE LEU PHE SEQRES 7 A 424 SER VAL SER GLU PHE MET PHE ALA VAL GLY HIS ASN PHE SEQRES 8 A 424 SER VAL LEU MET LEU SER ARG VAL ILE GLY GLY MET SER SEQRES 9 A 424 ALA GLY MET VAL MET PRO GLY VAL THR GLY LEU ILE ALA SEQRES 10 A 424 ASP ILE SER PRO SER HIS GLN LYS ALA LYS ASN PHE GLY SEQRES 11 A 424 TYR MET SER ALA ILE ILE ASN SER GLY PHE ILE LEU GLY SEQRES 12 A 424 PRO GLY ILE GLY GLY PHE MET ALA GLU VAL SER HIS ARG SEQRES 13 A 424 MET PRO PHE TYR PHE ALA GLY ALA LEU GLY ILE LEU ALA SEQRES 14 A 424 PHE ILE MET SER ILE VAL LEU ILE HIS ASP PRO LYS LYS SEQRES 15 A 424 SER THR THR SER GLY PHE GLN LYS LEU GLU PRO GLN LEU SEQRES 16 A 424 LEU THR LYS ILE ASN TRP LYS VAL PHE ILE THR PRO VAL SEQRES 17 A 424 ILE LEU THR LEU VAL LEU SER PHE GLY LEU SER ALA PHE SEQRES 18 A 424 GLN THR LEU TYR SER LEU TYR THR ALA ASP LYS VAL ASN SEQRES 19 A 424 TYR SER PRO LYS ASP ILE SER ILE ALA ILE THR GLY GLY SEQRES 20 A 424 GLY ILE PHE GLY ALA LEU PHE GLN ILE TYR PHE PHE ASP SEQRES 21 A 424 LYS PHE MET LYS TYR PHE SER GLU LEU THR PHE ILE ALA SEQRES 22 A 424 TRP SER LEU LEU TYR SER VAL VAL VAL LEU ILE LEU LEU SEQRES 23 A 424 VAL PHE ALA ASN ASP TYR TRP SER ILE MET LEU ILE SER SEQRES 24 A 424 PHE VAL VAL PHE ILE GLY PHE ASP MET ILE ARG PRO ALA SEQRES 25 A 424 ILE THR ASN TYR PHE SER ASN ILE ALA GLY GLU ARG GLN SEQRES 26 A 424 GLY PHE ALA GLY GLY LEU ASN SER THR PHE THR SER MET SEQRES 27 A 424 GLY ASN PHE ILE GLY PRO LEU ILE ALA GLY ALA LEU PHE SEQRES 28 A 424 ASP VAL HIS ILE GLU ALA PRO ILE TYR MET ALA ILE GLY SEQRES 29 A 424 VAL SER LEU ALA GLY VAL VAL ILE VAL LEU ILE GLU LYS SEQRES 30 A 424 GLN HIS ARG ALA LYS LEU LYS GLU GLN ASN MET GLU ASN SEQRES 31 A 424 LEU TYR PHE GLN GLY LYS LEU GLY PRO GLU GLN LYS LEU SEQRES 32 A 424 ILE SER GLU GLU ASP LEU ASN SER ALA VAL ASP HIS HIS SEQRES 33 A 424 HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 C 15 SER VAL GLU ASN HIS TRP TYR TYR PHE TYR TRP TYR MET SEQRES 2 C 15 SER PRO HELIX 1 AA1 ASN A 2 LEU A 21 1 20 HELIX 2 AA2 VAL A 22 PRO A 24 5 3 HELIX 3 AA3 VAL A 25 GLY A 34 1 10 HELIX 4 AA4 THR A 36 LEU A 65 1 30 HELIX 5 AA5 GLY A 66 VAL A 87 1 22 HELIX 6 AA6 ASN A 90 SER A 120 1 31 HELIX 7 AA7 GLN A 124 ILE A 141 1 18 HELIX 8 AA8 ILE A 141 ALA A 151 1 11 HELIX 9 AA9 ARG A 156 ILE A 177 1 22 HELIX 10 AB1 PHE A 204 LYS A 232 1 29 HELIX 11 AB2 SER A 236 LYS A 264 1 29 HELIX 12 AB3 SER A 267 PHE A 288 1 22 HELIX 13 AB4 ASP A 291 PHE A 300 1 10 HELIX 14 AB5 VAL A 301 GLY A 322 1 22 HELIX 15 AB6 ARG A 324 HIS A 354 1 31 HELIX 16 AB7 GLU A 356 GLN A 386 1 31 SHEET 1 AA1 2 ASN C 129 TYR C 132 0 SHEET 2 AA1 2 TYR C 135 MET C 138 -1 O TYR C 137 N HIS C 130 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