HEADER TRANSPORT PROTEIN 07-MAY-15 4ZOW TITLE CRYSTAL STRUCTURE OF E. COLI MULTIDRUG TRANSPORTER MDFA IN COMPLEX TITLE 2 WITH CHLORAMPHENICOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIDRUG TRANSPORTER MDFA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 10-400; COMPND 5 SYNONYM: CHLORAMPHENICOL RESISTANCE PUMP CMR; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: MDFA, CMLA, CMR, B0842, JW0826; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS MFS FAMILY, MULTI-DRUG ANTIPORTER, MDFA, CM, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.C.ZHANG,J.HENG,Y.ZHAO,X.WANG REVDAT 5 20-MAR-24 4ZOW 1 REMARK REVDAT 4 19-FEB-20 4ZOW 1 REMARK REVDAT 3 16-SEP-15 4ZOW 1 JRNL REVDAT 2 02-SEP-15 4ZOW 1 REMARK REVDAT 1 19-AUG-15 4ZOW 0 JRNL AUTH J.HENG,Y.ZHAO,M.LIU,Y.LIU,J.FAN,X.WANG,Y.ZHAO,X.C.ZHANG JRNL TITL SUBSTRATE-BOUND STRUCTURE OF THE E. COLI MULTIDRUG JRNL TITL 2 RESISTANCE TRANSPORTER MDFA JRNL REF CELL RES. V. 25 1060 2015 JRNL REFN ISSN 1001-0602 JRNL PMID 26238402 JRNL DOI 10.1038/CR.2015.94 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX PHENIX.REFINE: 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 21212 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1051 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.0953 - 4.8530 1.00 2600 150 0.2062 0.2365 REMARK 3 2 4.8530 - 3.8527 1.00 2583 131 0.1910 0.1929 REMARK 3 3 3.8527 - 3.3658 1.00 2537 127 0.1956 0.2190 REMARK 3 4 3.3658 - 3.0582 1.00 2592 110 0.2028 0.2687 REMARK 3 5 3.0582 - 2.8390 1.00 2519 124 0.1950 0.2438 REMARK 3 6 2.8390 - 2.6717 1.00 2546 128 0.2099 0.2651 REMARK 3 7 2.6717 - 2.5379 0.99 2469 160 0.2374 0.3027 REMARK 3 8 2.5379 - 2.4274 0.91 2315 121 0.2769 0.3317 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.39 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 3052 REMARK 3 ANGLE : 0.844 4154 REMARK 3 CHIRALITY : 0.060 497 REMARK 3 PLANARITY : 0.003 506 REMARK 3 DIHEDRAL : 13.672 1054 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ZOW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209639. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21233 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.99600 REMARK 200 R SYM FOR SHELL (I) : NULL 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: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, PEG 400, MAGNESIUM REMARK 280 ACETATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 46.92600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.72450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.92600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.72450 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 ARG A 10 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 11 CG CD1 CD2 REMARK 470 ARG A 13 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 14 CG CD OE1 NE2 REMARK 470 ARG A 131 CG CD NE CZ NH1 NH2 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 GLN A 103 -13.14 69.70 REMARK 500 ALA A 191 -60.87 -120.89 REMARK 500 REMARK 500 REMARK: NULL 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 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZP0 RELATED DB: PDB REMARK 900 RELATED ID: 4ZP2 RELATED DB: PDB DBREF 4ZOW A 10 400 UNP P0AEY8 MDFA_ECOLI 10 400 SEQADV 4ZOW ARG A 131 UNP P0AEY8 GLN 131 ENGINEERED MUTATION SEQRES 1 A 391 ARG LEU GLY ARG GLN ALA LEU LEU PHE PRO LEU CYS LEU SEQRES 2 A 391 VAL LEU TYR GLU PHE SER THR TYR ILE GLY ASN ASP MET SEQRES 3 A 391 ILE GLN PRO GLY MET LEU ALA VAL VAL GLU GLN TYR GLN SEQRES 4 A 391 ALA GLY ILE ASP TRP VAL PRO THR SER MET THR ALA TYR SEQRES 5 A 391 LEU ALA GLY GLY MET PHE LEU GLN TRP LEU LEU GLY PRO SEQRES 6 A 391 LEU SER ASP ARG ILE GLY ARG ARG PRO VAL MET LEU ALA SEQRES 7 A 391 GLY VAL VAL TRP PHE ILE VAL THR CYS LEU ALA ILE LEU SEQRES 8 A 391 LEU ALA GLN ASN ILE GLU GLN PHE THR LEU LEU ARG PHE SEQRES 9 A 391 LEU GLN GLY ILE SER LEU CYS PHE ILE GLY ALA VAL GLY SEQRES 10 A 391 TYR ALA ALA ILE ARG GLU SER PHE GLU GLU ALA VAL CYS SEQRES 11 A 391 ILE LYS ILE THR ALA LEU MET ALA ASN VAL ALA LEU ILE SEQRES 12 A 391 ALA PRO LEU LEU GLY PRO LEU VAL GLY ALA ALA TRP ILE SEQRES 13 A 391 HIS VAL LEU PRO TRP GLU GLY MET PHE VAL LEU PHE ALA SEQRES 14 A 391 ALA LEU ALA ALA ILE SER PHE PHE GLY LEU GLN ARG ALA SEQRES 15 A 391 MET PRO GLU THR ALA THR ARG ILE GLY GLU LYS LEU SER SEQRES 16 A 391 LEU LYS GLU LEU GLY ARG ASP TYR LYS LEU VAL LEU LYS SEQRES 17 A 391 ASN GLY ARG PHE VAL ALA GLY ALA LEU ALA LEU GLY PHE SEQRES 18 A 391 VAL SER LEU PRO LEU LEU ALA TRP ILE ALA GLN SER PRO SEQRES 19 A 391 ILE ILE ILE ILE THR GLY GLU GLN LEU SER SER TYR GLU SEQRES 20 A 391 TYR GLY LEU LEU GLN VAL PRO ILE PHE GLY ALA LEU ILE SEQRES 21 A 391 ALA GLY ASN LEU LEU LEU ALA ARG LEU THR SER ARG ARG SEQRES 22 A 391 THR VAL ARG SER LEU ILE ILE MET GLY GLY TRP PRO ILE SEQRES 23 A 391 MET ILE GLY LEU LEU VAL ALA ALA ALA ALA THR VAL ILE SEQRES 24 A 391 SER SER HIS ALA TYR LEU TRP MET THR ALA GLY LEU SER SEQRES 25 A 391 ILE TYR ALA PHE GLY ILE GLY LEU ALA ASN ALA GLY LEU SEQRES 26 A 391 VAL ARG LEU THR LEU PHE ALA SER ASP MET SER LYS GLY SEQRES 27 A 391 THR VAL SER ALA ALA MET GLY MET LEU GLN MET LEU ILE SEQRES 28 A 391 PHE THR VAL GLY ILE GLU ILE SER LYS HIS ALA TRP LEU SEQRES 29 A 391 ASN GLY GLY ASN GLY LEU PHE ASN LEU PHE ASN LEU VAL SEQRES 30 A 391 ASN GLY ILE LEU TRP LEU SER LEU MET VAL ILE PHE LEU SEQRES 31 A 391 LYS HET CLM A 500 20 HETNAM CLM CHLORAMPHENICOL FORMUL 2 CLM C11 H12 CL2 N2 O5 FORMUL 3 HOH *13(H2 O) HELIX 1 AA1 ARG A 13 ALA A 15 5 3 HELIX 2 AA2 LEU A 16 MET A 35 1 20 HELIX 3 AA3 MET A 35 TYR A 47 1 13 HELIX 4 AA4 ASP A 52 MET A 66 1 15 HELIX 5 AA5 LEU A 68 GLY A 80 1 13 HELIX 6 AA6 GLY A 80 ILE A 99 1 20 HELIX 7 AA7 LEU A 100 ALA A 102 5 3 HELIX 8 AA8 ASN A 104 ILE A 117 1 14 HELIX 9 AA9 LEU A 119 VAL A 125 1 7 HELIX 10 AB1 VAL A 125 PHE A 134 1 10 HELIX 11 AB2 GLU A 135 ILE A 165 1 31 HELIX 12 AB3 TRP A 170 MET A 192 1 23 HELIX 13 AB4 SER A 204 LEU A 216 1 13 HELIX 14 AB5 ASN A 218 ILE A 247 1 30 HELIX 15 AB6 SER A 253 THR A 279 1 27 HELIX 16 AB7 THR A 283 SER A 309 1 27 HELIX 17 AB8 ALA A 312 ALA A 341 1 30 HELIX 18 AB9 SER A 345 LEU A 399 1 55 CISPEP 1 ILE A 199 GLY A 200 0 -1.83 CISPEP 2 LEU A 399 LYS A 400 0 -3.26 SITE 1 AC1 9 TYR A 30 ASN A 33 ASP A 34 MET A 58 SITE 2 AC1 9 LEU A 62 ALA A 150 LEU A 151 LEU A 236 SITE 3 AC1 9 ILE A 239 CRYST1 93.852 63.449 99.726 90.00 106.09 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 0.010655 0.000000 0.003074 0.00000 SCALE2 0.000000 0.015761 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010436 0.00000