HEADER TRANSPORT PROTEIN 31-JUL-13 4LZ9 TITLE STRUCTURE OF MATE MULTIDRUG TRANSPORTER DINF-BH IN COMPLEX WITH R6G COMPND MOL_ID: 1; COMPND 2 MOLECULE: BH2163 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 3-448; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: C-125; SOURCE 5 GENE: BH2163; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MULTIDRUG TRANSPORTER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR M.LU,M.RADCHENKO,J.SYMERSKY,R.NIE,Y.GUO REVDAT 3 20-MAR-24 4LZ9 1 REMARK REVDAT 2 20-NOV-13 4LZ9 1 JRNL REVDAT 1 23-OCT-13 4LZ9 0 JRNL AUTH M.LU,M.RADCHENKO,J.SYMERSKY,R.NIE,Y.GUO JRNL TITL STRUCTURAL INSIGHTS INTO H(+)-COUPLED MULTIDRUG EXTRUSION BY JRNL TITL 2 A MATE TRANSPORTER JRNL REF NAT.STRUCT.MOL.BIOL. V. 20 1310 2013 JRNL REFN ISSN 1545-9993 JRNL PMID 24141706 JRNL DOI 10.1038/NSMB.2687 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 8797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.300 REMARK 3 R VALUE (WORKING SET) : 0.290 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 440 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 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 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 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 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.011 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 2.000 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE COORDINATES CONTAIN ONLY A CA REMARK 3 TRACE. REMARK 4 REMARK 4 4LZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9220 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.700 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 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) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 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 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING 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 (%): 72.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, NACL, PH 8.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 45.09050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.13350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.94350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.13350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.09050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.94350 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RHQ A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LZ6 RELATED DB: PDB DBREF 4LZ9 A 3 448 UNP Q9KAX3 Q9KAX3_BACHD 3 448 SEQRES 1 A 446 GLN LYS GLN GLN SER GLU ARG LEU GLY THR GLU ALA ILE SEQRES 2 A 446 PRO LYS LEU LEU ARG SER LEU SER ILE PRO ALA MET ILE SEQRES 3 A 446 GLY MET PHE VAL MET ALA LEU TYR ASN VAL VAL ASP THR SEQRES 4 A 446 ILE PHE ILE SER TYR ALA VAL GLY ILE GLU GLY VAL ALA SEQRES 5 A 446 GLY VAL THR ILE ALA PHE PRO ILE MET MET ILE MET MET SEQRES 6 A 446 SER MET ALA GLY ALA LEU GLY ILE GLY GLY ALA SER VAL SEQRES 7 A 446 ILE SER ARG ARG LEU GLY GLU ARG ARG GLY GLU GLU ALA SEQRES 8 A 446 ASN GLN VAL PHE GLY ASN ILE LEU THR VAL ILE LEU VAL SEQRES 9 A 446 LEU SER VAL ILE GLY PHE ILE SER ALA PHE THR LEU LEU SEQRES 10 A 446 GLY PRO ALA LEU GLN LEU PHE GLY ALA THR SER VAL THR SEQRES 11 A 446 GLN GLY TYR ALA THR ASP TYR LEU PHE PRO ILE LEU LEU SEQRES 12 A 446 GLY SER ILE PHE PHE PHE PHE ALA PHE ALA ALA ASN ASN SEQRES 13 A 446 ILE ILE ARG SER GLU GLY ASN ALA THR PHE ALA MET VAL SEQRES 14 A 446 THR MET ILE VAL PRO ALA VAL LEU ASN ILE LEU LEU ASP SEQRES 15 A 446 VAL LEU PHE ILE PHE GLY LEU ASN MET GLY VAL LEU GLY SEQRES 16 A 446 ALA SER ILE ALA THR VAL ILE ALA GLN ALA SER VAL THR SEQRES 17 A 446 GLY LEU VAL LEU ARG TYR PHE LEU THR GLY LYS SER THR SEQRES 18 A 446 LEU SER LEU HIS TRP SER ASP LEU ARG MET LYS GLY SER SEQRES 19 A 446 VAL ILE LYS GLU VAL CYS LEU VAL GLY LEU PRO ALA PHE SEQRES 20 A 446 VAL GLN GLN SER SER ALA SER LEU MET MET ILE ALA ILE SEQRES 21 A 446 ASN SER MET LEU LEU ARG PHE GLY SER ASP PHE TYR VAL SEQRES 22 A 446 GLY VAL PHE GLY LEU VAL GLN ARG ILE MET MET PHE VAL SEQRES 23 A 446 MET MET PRO MET MET GLY ILE MET GLN ALA MET GLN PRO SEQRES 24 A 446 ILE VAL GLY TYR ASN TYR GLY ALA LYS GLN TYR SER ARG SEQRES 25 A 446 LEU ARG GLU THR VAL MET LEU GLY PHE LYS VAL ALA THR SEQRES 26 A 446 ILE PHE SER ILE GLY ILE PHE ALA LEU LEU MET LEU PHE SEQRES 27 A 446 PRO GLU ALA LEU LEU ARG VAL PHE THR ALA ASP ARG GLU SEQRES 28 A 446 VAL ILE GLN ALA GLY VAL SER ALA MET HIS ILE LEU PHE SEQRES 29 A 446 CYS VAL THR PHE LEU ILE GLY ALA GLN ILE VAL ALA GLY SEQRES 30 A 446 GLY LEU TYR GLN SER LEU GLY LYS PRO LYS GLN ALA LEU SEQRES 31 A 446 ILE LEU SER LEU SER ARG GLN ILE ILE PHE LEU ILE PRO SEQRES 32 A 446 LEU VAL LEU ILE LEU PRO HIS ILE PHE GLY LEU SER GLY SEQRES 33 A 446 VAL TRP TRP ALA PHE PRO ILE ALA ASP VAL LEU SER PHE SEQRES 34 A 446 ILE LEU THR VAL VAL LEU LEU TYR ARG ASP ARG ASN VAL SEQRES 35 A 446 PHE PHE LEU LYS HET RHQ A 501 33 HETNAM RHQ RHODAMINE 6G FORMUL 2 RHQ C28 H31 N2 O3 1+ SITE 1 AC1 1 ALA A 34 CRYST1 90.181 93.887 102.267 90.00 90.00 90.00 P 21 21 21 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 0.011089 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010651 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009778 0.00000