HEADER TRANSPORT PROTEIN 17-NOV-05 2F2M OBSLTE 12-DEC-06 2F2M TITLE X-RAY CRYSTAL STRUCTURE OF THE EMRE MULTIDRUG TRANSPORTER IN COMPLEX TITLE 2 WITH TPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN EMRE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METHYL VIOLOGEN RESISTANCE PROTEIN C, ETHIDIUM RESISTANCE COMPND 5 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: EMRE, EB, MVRC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS MULTIDRUG TRANSPORTER, ANTIPARALLEL DIMER, TRANSPORTER-SUBSTRATE KEYWDS 2 COMPLEX, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR O.PORNILLOS,Y.J.CHEN,A.P.CHEN,G.CHANG REVDAT 5 23-MAY-12 2F2M 1 JRNL REVDAT 4 02-MAY-12 2F2M 1 REMARK REVDAT 3 12-DEC-06 2F2M 1 OBSLTE REVDAT 2 10-JAN-06 2F2M 1 JRNL REVDAT 1 27-DEC-05 2F2M 0 JRNL AUTH O.PORNILLOS,Y.J.CHEN,A.P.CHEN,G.CHANG JRNL TITL RETRACTION JRNL REF SCIENCE V. 314 1875 2006 JRNL REFN ISSN 0036-8075 JRNL DOI 10.1126/SCIENCE.314.5807.1875B REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.PORNILLOS,Y.J.CHEN,A.P.CHEN,G.CHANG REMARK 1 TITL X-RAY STRUCTURE OF THE EMRE MULTIDRUG TRANSPORTER IN COMPLEX REMARK 1 TITL 2 WITH A SUBSTRATE REMARK 1 REF SCIENCE V. 310 1950 2005 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 16373573 REMARK 1 DOI 10.1126/SCIENCE.1119776 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 2555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : R FREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.282 REMARK 3 FREE R VALUE : 0.354 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 255 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1614 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 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) : NULL 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 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) : 0.030 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 0.02 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 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: B VALUES SET UNIFORMLY TO 40% REMARK 4 REMARK 4 2F2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 STRUCTURE WAS OBSOLETED DUE TO PAPER RETRACTION REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-05. REMARK 100 THE RCSB ID CODE IS RCSB035375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-05; 01-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0; NULL REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : APS/SSRL; NULL REMARK 200 BEAMLINE : 19-ID/11-1; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.00443; NULL REMARK 200 MONOCHROMATOR : BENDING MAGNET; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2555 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 64.0 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-3MM PROTEIN, 11-14% PEG2000 MME, 100 REMARK 280 MM TRIS-HCL, 100-200 MM CACL2, 0.35% NONYLGLUCOSIDE, PH 6.4-6.8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, PH 6.80 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 57.41600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.85050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.41600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.85050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: NULL 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 300 REMARK: EACH ASYMMETRIC UNIT REPRESENTS THE PUTATIVE STRUCTURAL AND REMARK 300 FUNCTIONAL UNIT OF THE EMRE TRANSPORTER. 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 PRO A 3 REMARK 465 TYR A 4 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 PRO B 3 REMARK 465 TYR B 4 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 TYR A 6 -81.52 -34.95 REMARK 500 ALA A 13 -79.03 -58.54 REMARK 500 GLU A 14 -46.59 -28.44 REMARK 500 VAL A 15 -74.69 -63.10 REMARK 500 THR A 28 -157.67 -76.89 REMARK 500 ARG A 29 85.50 69.46 REMARK 500 LEU A 30 36.02 89.71 REMARK 500 PRO A 32 -121.25 -53.25 REMARK 500 ALA A 52 96.56 -67.13 REMARK 500 TYR A 53 91.81 -47.06 REMARK 500 ILE A 54 -56.26 -146.41 REMARK 500 ILE A 58 36.90 -98.47 REMARK 500 ALA A 61 -59.71 -20.79 REMARK 500 ASP A 84 78.25 -59.61 REMARK 500 THR A 108 -62.49 -132.97 REMARK 500 GLU B 25 34.73 -99.27 REMARK 500 THR B 28 71.96 -159.90 REMARK 500 LEU B 30 151.81 177.86 REMARK 500 PRO B 32 -35.53 -36.19 REMARK 500 SER B 33 -76.22 -48.66 REMARK 500 ILE B 54 96.97 169.60 REMARK 500 LEU B 83 57.69 38.35 REMARK 500 ASP B 84 86.73 7.14 REMARK 500 SER B 107 -74.31 -72.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 30 22.2 L L OUTSIDE RANGE 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 P4P A 201 DBREF 2F2M A 1 110 UNP P23895 EMRE_ECOLI 1 110 DBREF 2F2M B 1 110 UNP P23895 EMRE_ECOLI 1 110 SEQADV 2F2M GLY A -2 UNP P23895 CLONING ARTIFACT SEQADV 2F2M SER A -1 UNP P23895 CLONING ARTIFACT SEQADV 2F2M HIS A 0 UNP P23895 CLONING ARTIFACT SEQADV 2F2M GLY B -2 UNP P23895 CLONING ARTIFACT SEQADV 2F2M SER B -1 UNP P23895 CLONING ARTIFACT SEQADV 2F2M HIS B 0 UNP P23895 CLONING ARTIFACT SEQRES 1 A 113 GLY SER HIS MET ASN PRO TYR ILE TYR LEU GLY GLY ALA SEQRES 2 A 113 ILE LEU ALA GLU VAL ILE GLY THR THR LEU MET LYS PHE SEQRES 3 A 113 SER GLU GLY PHE THR ARG LEU TRP PRO SER VAL GLY THR SEQRES 4 A 113 ILE ILE CYS TYR CYS ALA SER PHE TRP LEU LEU ALA GLN SEQRES 5 A 113 THR LEU ALA TYR ILE PRO THR GLY ILE ALA TYR ALA ILE SEQRES 6 A 113 TRP SER GLY VAL GLY ILE VAL LEU ILE SER LEU LEU SER SEQRES 7 A 113 TRP GLY PHE PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE SEQRES 8 A 113 ILE GLY MET MET LEU ILE CYS ALA GLY VAL LEU ILE ILE SEQRES 9 A 113 ASN LEU LEU SER ARG SER THR PRO HIS SEQRES 1 B 113 GLY SER HIS MET ASN PRO TYR ILE TYR LEU GLY GLY ALA SEQRES 2 B 113 ILE LEU ALA GLU VAL ILE GLY THR THR LEU MET LYS PHE SEQRES 3 B 113 SER GLU GLY PHE THR ARG LEU TRP PRO SER VAL GLY THR SEQRES 4 B 113 ILE ILE CYS TYR CYS ALA SER PHE TRP LEU LEU ALA GLN SEQRES 5 B 113 THR LEU ALA TYR ILE PRO THR GLY ILE ALA TYR ALA ILE SEQRES 6 B 113 TRP SER GLY VAL GLY ILE VAL LEU ILE SER LEU LEU SER SEQRES 7 B 113 TRP GLY PHE PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE SEQRES 8 B 113 ILE GLY MET MET LEU ILE CYS ALA GLY VAL LEU ILE ILE SEQRES 9 B 113 ASN LEU LEU SER ARG SER THR PRO HIS HET P4P A 201 25 HETNAM P4P TETRAPHENYLPHOSPHONIUM FORMUL 3 P4P C24 H20 P 1+ HELIX 1 1 ILE A 5 THR A 28 1 24 HELIX 2 2 TRP A 31 ALA A 52 1 22 HELIX 3 3 TYR A 60 GLY A 77 1 18 HELIX 4 4 LEU A 85 THR A 108 1 24 HELIX 5 5 ILE B 5 GLU B 25 1 21 HELIX 6 6 TRP B 31 ALA B 52 1 22 HELIX 7 7 GLY B 57 PHE B 79 1 23 HELIX 8 8 ALA B 87 THR B 108 1 22 SITE 1 AC1 6 ALA A 13 GLU A 14 ILE A 16 GLY A 17 SITE 2 AC1 6 LEU A 20 LEU A 47 CRYST1 114.832 43.701 75.685 90.00 108.76 90.00 C 1 2 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 0.008708 0.000000 0.002958 0.00000 SCALE2 0.000000 0.022883 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013954 0.00000