HEADER TRANSPORT PROTEIN/ANTIBIOTIC 10-FEB-20 6VRZ TITLE PROTEIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIDRUG TRANSPORTER MDFA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHLORAMPHENICOL RESISTANCE PUMP CMR; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MDFA, CMLA, CMR, B0842, JW0826; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE PROTEIN, TRANSPORT PROTEIN-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.LU,M.M.LU REVDAT 2 06-MAR-24 6VRZ 1 REMARK REVDAT 1 03-JUN-20 6VRZ 0 JRNL AUTH H.H.WU,J.SYMERSKY,M.LU JRNL TITL STRUCTURE AND MECHANISM OF A REDESIGNED MULTIDRUG JRNL TITL 2 TRANSPORTER FROM THE MAJOR FACILITATOR SUPERFAMILY. JRNL REF SCI REP V. 10 3949 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32127561 JRNL DOI 10.1038/S41598-020-60332-8 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 2.1 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 39352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2937 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39352 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 31.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.67000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, SALTS, MAGNESIUM, ETC, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.52400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.60750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.52400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.60750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 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 GLN A 14 CG CD OE1 NE2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 695 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 696 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 697 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A 698 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 699 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 700 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A 701 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A 702 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A 703 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 704 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A 705 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A 706 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH A 707 DISTANCE = 7.56 ANGSTROMS REMARK 525 HOH A 708 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH A 709 DISTANCE = 7.86 ANGSTROMS REMARK 525 HOH A 710 DISTANCE = 8.28 ANGSTROMS REMARK 525 HOH A 711 DISTANCE = 8.75 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CLM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PR A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PR A 503 DBREF 6VRZ A 14 400 UNP P0AEY8 MDFA_ECOLI 14 400 SEQADV 6VRZ THR A 26 UNP P0AEY8 GLU 26 ENGINEERED MUTATION SEQADV 6VRZ MET A 34 UNP P0AEY8 ASP 34 ENGINEERED MUTATION SEQADV 6VRZ GLU A 150 UNP P0AEY8 ALA 150 ENGINEERED MUTATION SEQRES 1 A 387 GLN ALA LEU LEU PHE PRO LEU CYS LEU VAL LEU TYR THR SEQRES 2 A 387 PHE SER THR TYR ILE GLY ASN MET MET ILE GLN PRO GLY SEQRES 3 A 387 MET LEU ALA VAL VAL GLU GLN TYR GLN ALA GLY ILE ASP SEQRES 4 A 387 TRP VAL PRO THR SER MET THR ALA TYR LEU ALA GLY GLY SEQRES 5 A 387 MET PHE LEU GLN TRP LEU LEU GLY PRO LEU SER ASP ARG SEQRES 6 A 387 ILE GLY ARG ARG PRO VAL MET LEU ALA GLY VAL VAL TRP SEQRES 7 A 387 PHE ILE VAL THR CYS LEU ALA ILE LEU LEU ALA GLN ASN SEQRES 8 A 387 ILE GLU GLN PHE THR LEU LEU ARG PHE LEU GLN GLY ILE SEQRES 9 A 387 SER LEU CYS PHE ILE GLY ALA VAL GLY TYR ALA ALA ILE SEQRES 10 A 387 GLN GLU SER PHE GLU GLU ALA VAL CYS ILE LYS ILE THR SEQRES 11 A 387 ALA LEU MET ALA ASN VAL GLU LEU ILE ALA PRO LEU LEU SEQRES 12 A 387 GLY PRO LEU VAL GLY ALA ALA TRP ILE HIS VAL LEU PRO SEQRES 13 A 387 TRP GLU GLY MET PHE VAL LEU PHE ALA ALA LEU ALA ALA SEQRES 14 A 387 ILE SER PHE PHE GLY LEU GLN ARG ALA MET PRO GLU THR SEQRES 15 A 387 ALA THR ARG ILE GLY GLU LYS LEU SER LEU LYS GLU LEU SEQRES 16 A 387 GLY ARG ASP TYR LYS LEU VAL LEU LYS ASN GLY ARG PHE SEQRES 17 A 387 VAL ALA GLY ALA LEU ALA LEU GLY PHE VAL SER LEU PRO SEQRES 18 A 387 LEU LEU ALA TRP ILE ALA GLN SER PRO ILE ILE ILE ILE SEQRES 19 A 387 THR GLY GLU GLN LEU SER SER TYR GLU TYR GLY LEU LEU SEQRES 20 A 387 GLN VAL PRO ILE PHE GLY ALA LEU ILE ALA GLY ASN LEU SEQRES 21 A 387 LEU LEU ALA ARG LEU THR SER ARG ARG THR VAL ARG SER SEQRES 22 A 387 LEU ILE ILE MET GLY GLY TRP PRO ILE MET ILE GLY LEU SEQRES 23 A 387 LEU VAL ALA ALA ALA ALA THR VAL ILE SER SER HIS ALA SEQRES 24 A 387 TYR LEU TRP MET THR ALA GLY LEU SER ILE TYR ALA PHE SEQRES 25 A 387 GLY ILE GLY LEU ALA ASN ALA GLY LEU VAL ARG LEU THR SEQRES 26 A 387 LEU PHE ALA SER ASP MET SER LYS GLY THR VAL SER ALA SEQRES 27 A 387 ALA MET GLY MET LEU GLN MET LEU ILE PHE THR VAL GLY SEQRES 28 A 387 ILE GLU ILE SER LYS HIS ALA TRP LEU ASN GLY GLY ASN SEQRES 29 A 387 GLY LEU PHE ASN LEU PHE ASN LEU VAL ASN GLY ILE LEU SEQRES 30 A 387 TRP LEU SER LEU MET VAL ILE PHE LEU LYS HET CLM A 501 20 HET PR A 502 1 HET PR A 503 1 HETNAM CLM CHLORAMPHENICOL HETNAM PR PRASEODYMIUM ION FORMUL 2 CLM C11 H12 CL2 N2 O5 FORMUL 3 PR 2(PR 3+) FORMUL 5 HOH *111(H2 O) HELIX 1 AA1 LEU A 16 MET A 35 1 20 HELIX 2 AA2 MET A 35 GLN A 48 1 14 HELIX 3 AA3 ASP A 52 LEU A 68 1 17 HELIX 4 AA4 LEU A 68 GLY A 80 1 13 HELIX 5 AA5 GLY A 80 ILE A 99 1 20 HELIX 6 AA6 LEU A 100 ALA A 102 5 3 HELIX 7 AA7 ASN A 104 ILE A 117 1 14 HELIX 8 AA8 CYS A 120 VAL A 125 1 6 HELIX 9 AA9 VAL A 125 PHE A 134 1 10 HELIX 10 AB1 GLU A 135 LEU A 168 1 34 HELIX 11 AB2 PRO A 169 MET A 192 1 24 HELIX 12 AB3 SER A 204 ASN A 218 1 15 HELIX 13 AB4 ASN A 218 ILE A 247 1 30 HELIX 14 AB5 SER A 253 THR A 279 1 27 HELIX 15 AB6 THR A 283 SER A 309 1 27 HELIX 16 AB7 ALA A 312 PHE A 340 1 29 HELIX 17 AB8 SER A 345 LEU A 399 1 55 LINK O GLU A 207 PR PR A 503 1555 1555 3.31 LINK OD2 ASP A 211 PR PR A 502 1555 1555 3.37 SITE 1 AC1 6 TYR A 30 LEU A 62 LEU A 119 GLU A 150 SITE 2 AC1 6 SER A 232 GLN A 357 SITE 1 AC2 1 ASP A 211 SITE 1 AC3 2 GLU A 207 SER A 253 CRYST1 95.048 65.215 111.462 90.00 111.32 90.00 C 1 2 1 4 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 0.010521 0.000000 0.004106 0.00000 SCALE2 0.000000 0.015334 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.009631 0.00000