HEADER MEMBRANE PROTEIN 26-OCT-07 3B62 TITLE EMRE MULTIDRUG TRANSPORTER IN COMPLEX WITH P4P, P21 CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIDRUG TRANSPORTER EMRE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: EFFLUX-MULTIDRUG RESISTANCE PROTEIN EMRE, METHYL VIOLOGEN COMPND 5 RESISTANCE PROTEIN C, ETHIDIUM RESISTANCE PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: EMRE, EB, MVRC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PIVEX KEYWDS HELICAL MEMBRANE PROTEIN, MULTIDRUG RESISTANCE TRANSPORTER, SMR, KEYWDS 2 ANTIPORT, INNER MEMBRANE, TRANSMEMBRANE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A, B, C, D AUTHOR G.CHANG,Y.J.CHEN REVDAT 4 21-FEB-24 3B62 1 REMARK REVDAT 3 24-FEB-09 3B62 1 VERSN REVDAT 2 26-FEB-08 3B62 1 JRNL REVDAT 1 04-DEC-07 3B62 0 JRNL AUTH Y.J.CHEN,O.PORNILLOS,S.LIEU,C.MA,A.P.CHEN,G.CHANG JRNL TITL X-RAY STRUCTURE OF EMRE SUPPORTS DUAL TOPOLOGY MODEL. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 18999 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 18024586 JRNL DOI 10.1073/PNAS.0709387104 REMARK 2 REMARK 2 RESOLUTION. 4.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 72.9 REMARK 3 NUMBER OF REFLECTIONS : 3394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.343 REMARK 3 FREE R VALUE : 0.364 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 345 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 4.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3670 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 55 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.053 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 182.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -99.05000 REMARK 3 B22 (A**2) : 63.92000 REMARK 3 B33 (A**2) : 35.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE CONTAINS CA ATOMS ONLY. REMARK 4 REMARK 4 3B62 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045123. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790, 0.9793, 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3394 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42800 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100-200 MM CALCIUM CHLORIDE, 100 MM REMARK 280 TRIS, 11-14% (W/V) PEG 2,000 MME, AND 0.3-0.6% (W/V) NG, PH 6.8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.35000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 PRO A 3 REMARK 465 TYR A 4 REMARK 465 ILE A 5 REMARK 465 TYR A 6 REMARK 465 ASN A 102 REMARK 465 LEU A 103 REMARK 465 LEU A 104 REMARK 465 SER A 105 REMARK 465 ARG A 106 REMARK 465 SER A 107 REMARK 465 THR A 108 REMARK 465 PRO A 109 REMARK 465 HIS A 110 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 PRO B 3 REMARK 465 TYR B 4 REMARK 465 ILE B 5 REMARK 465 TYR B 6 REMARK 465 ILE B 94 REMARK 465 CYS B 95 REMARK 465 ALA B 96 REMARK 465 GLY B 97 REMARK 465 VAL B 98 REMARK 465 LEU B 99 REMARK 465 ILE B 100 REMARK 465 ILE B 101 REMARK 465 ASN B 102 REMARK 465 LEU B 103 REMARK 465 LEU B 104 REMARK 465 SER B 105 REMARK 465 ARG B 106 REMARK 465 SER B 107 REMARK 465 THR B 108 REMARK 465 PRO B 109 REMARK 465 HIS B 110 REMARK 465 MET C 1 REMARK 465 ASN C 2 REMARK 465 PRO C 3 REMARK 465 TYR C 4 REMARK 465 ILE C 5 REMARK 465 TYR C 6 REMARK 465 ASN C 102 REMARK 465 LEU C 103 REMARK 465 LEU C 104 REMARK 465 SER C 105 REMARK 465 ARG C 106 REMARK 465 SER C 107 REMARK 465 THR C 108 REMARK 465 PRO C 109 REMARK 465 HIS C 110 REMARK 465 MET D 1 REMARK 465 ASN D 2 REMARK 465 PRO D 3 REMARK 465 TYR D 4 REMARK 465 ILE D 5 REMARK 465 TYR D 6 REMARK 465 ILE D 94 REMARK 465 CYS D 95 REMARK 465 ALA D 96 REMARK 465 GLY D 97 REMARK 465 VAL D 98 REMARK 465 LEU D 99 REMARK 465 ILE D 100 REMARK 465 ILE D 101 REMARK 465 ASN D 102 REMARK 465 LEU D 103 REMARK 465 LEU D 104 REMARK 465 SER D 105 REMARK 465 ARG D 106 REMARK 465 SER D 107 REMARK 465 THR D 108 REMARK 465 PRO D 109 REMARK 465 HIS D 110 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P4P A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P4P C 750 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B5D RELATED DB: PDB REMARK 900 EMRE-TPP STRUCTURE, C2 CRYSTAL FORM REMARK 900 RELATED ID: 3B61 RELATED DB: PDB DBREF 3B62 A 1 110 UNP P23895 EMRE_ECOLI 1 110 DBREF 3B62 B 1 110 UNP P23895 EMRE_ECOLI 1 110 DBREF 3B62 C 1 110 UNP P23895 EMRE_ECOLI 1 110 DBREF 3B62 D 1 110 UNP P23895 EMRE_ECOLI 1 110 SEQRES 1 A 110 MET ASN PRO TYR ILE TYR LEU GLY GLY ALA ILE LEU ALA SEQRES 2 A 110 GLU VAL ILE GLY THR THR LEU MET LYS PHE SER GLU GLY SEQRES 3 A 110 PHE THR ARG LEU TRP PRO SER VAL GLY THR ILE ILE CYS SEQRES 4 A 110 TYR CYS ALA SER PHE TRP LEU LEU ALA GLN THR LEU ALA SEQRES 5 A 110 TYR ILE PRO THR GLY ILE ALA TYR ALA ILE TRP SER GLY SEQRES 6 A 110 VAL GLY ILE VAL LEU ILE SER LEU LEU SER TRP GLY PHE SEQRES 7 A 110 PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE ILE GLY MET SEQRES 8 A 110 MET LEU ILE CYS ALA GLY VAL LEU ILE ILE ASN LEU LEU SEQRES 9 A 110 SER ARG SER THR PRO HIS SEQRES 1 B 110 MET ASN PRO TYR ILE TYR LEU GLY GLY ALA ILE LEU ALA SEQRES 2 B 110 GLU VAL ILE GLY THR THR LEU MET LYS PHE SER GLU GLY SEQRES 3 B 110 PHE THR ARG LEU TRP PRO SER VAL GLY THR ILE ILE CYS SEQRES 4 B 110 TYR CYS ALA SER PHE TRP LEU LEU ALA GLN THR LEU ALA SEQRES 5 B 110 TYR ILE PRO THR GLY ILE ALA TYR ALA ILE TRP SER GLY SEQRES 6 B 110 VAL GLY ILE VAL LEU ILE SER LEU LEU SER TRP GLY PHE SEQRES 7 B 110 PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE ILE GLY MET SEQRES 8 B 110 MET LEU ILE CYS ALA GLY VAL LEU ILE ILE ASN LEU LEU SEQRES 9 B 110 SER ARG SER THR PRO HIS SEQRES 1 C 110 MET ASN PRO TYR ILE TYR LEU GLY GLY ALA ILE LEU ALA SEQRES 2 C 110 GLU VAL ILE GLY THR THR LEU MET LYS PHE SER GLU GLY SEQRES 3 C 110 PHE THR ARG LEU TRP PRO SER VAL GLY THR ILE ILE CYS SEQRES 4 C 110 TYR CYS ALA SER PHE TRP LEU LEU ALA GLN THR LEU ALA SEQRES 5 C 110 TYR ILE PRO THR GLY ILE ALA TYR ALA ILE TRP SER GLY SEQRES 6 C 110 VAL GLY ILE VAL LEU ILE SER LEU LEU SER TRP GLY PHE SEQRES 7 C 110 PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE ILE GLY MET SEQRES 8 C 110 MET LEU ILE CYS ALA GLY VAL LEU ILE ILE ASN LEU LEU SEQRES 9 C 110 SER ARG SER THR PRO HIS SEQRES 1 D 110 MET ASN PRO TYR ILE TYR LEU GLY GLY ALA ILE LEU ALA SEQRES 2 D 110 GLU VAL ILE GLY THR THR LEU MET LYS PHE SER GLU GLY SEQRES 3 D 110 PHE THR ARG LEU TRP PRO SER VAL GLY THR ILE ILE CYS SEQRES 4 D 110 TYR CYS ALA SER PHE TRP LEU LEU ALA GLN THR LEU ALA SEQRES 5 D 110 TYR ILE PRO THR GLY ILE ALA TYR ALA ILE TRP SER GLY SEQRES 6 D 110 VAL GLY ILE VAL LEU ILE SER LEU LEU SER TRP GLY PHE SEQRES 7 D 110 PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE ILE GLY MET SEQRES 8 D 110 MET LEU ILE CYS ALA GLY VAL LEU ILE ILE ASN LEU LEU SEQRES 9 D 110 SER ARG SER THR PRO HIS HET P4P A 350 25 HET P4P C 750 25 HETNAM P4P TETRAPHENYLPHOSPHONIUM FORMUL 5 P4P 2(C24 H20 P 1+) SITE 1 AC1 1 PHE A 44 SITE 1 AC2 1 PHE C 44 CRYST1 76.500 42.700 115.400 90.00 109.10 90.00 P 1 21 1 8 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 0.013072 0.000000 0.004527 0.00000 SCALE2 0.000000 0.023419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009170 0.00000