HEADER TRANSCRIPTION 04-JUN-01 1JBG TITLE CRYSTAL STRUCTURE OF MTAN, THE BACILLUS SUBTILIS MULTIDRUG TRANSPORTER TITLE 2 ACTIVATOR, N-TERMINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION ACTIVATOR OF MULTIDRUG-EFFLUX TRANSPORTER COMPND 3 GENES MTA; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: N-TERMINUS (RESIDUES 1-109); COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: LMG194; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBAD-MYC-HIS KEYWDS WINGED HELIX-TURN-HELIX, ANTIPARALLEL COILED-COIL, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.H.GODSEY,A.A.NEYFAKH,R.G.BRENNAN REVDAT 5 07-FEB-24 1JBG 1 REMARK REVDAT 4 13-JUL-11 1JBG 1 VERSN REVDAT 3 24-FEB-09 1JBG 1 VERSN REVDAT 2 01-APR-03 1JBG 1 JRNL REVDAT 1 28-NOV-01 1JBG 0 JRNL AUTH M.H.GODSEY,N.N.BARANOVA,A.A.NEYFAKH,R.G.BRENNAN JRNL TITL CRYSTAL STRUCTURE OF MTAN, A GLOBAL MULTIDRUG TRANSPORTER JRNL TITL 2 GENE ACTIVATOR. JRNL REF J.BIOL.CHEM. V. 276 47178 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11581256 JRNL DOI 10.1074/JBC.M105819200 REMARK 2 REMARK 2 RESOLUTION. 2.75 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 157528.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 4812 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) : 0.228 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 261 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.018 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 654 REMARK 3 BIN R VALUE (WORKING SET) : 0.4000 REMARK 3 BIN FREE R VALUE : 0.5270 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 36 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.088 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 861 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 121.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.30000 REMARK 3 B22 (A**2) : 45.44000 REMARK 3 B33 (A**2) : -40.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM SIGMAA (A) : 0.57 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.56 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC, RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.120 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.840 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.820 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 43.17 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JBG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013585. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : 58 CM LONG, PT-COATED, FUSED REMARK 200 SILICA, VERTICAL FOCUS MIRROR; REMARK 200 CYCLINDRICALLY BENT TRIANGULAR REMARK 200 SI(111) ASYMMETRIC CUT, REMARK 200 HORIZONTAL FOCUS MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5199 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 23.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.27100 REMARK 200 R SYM FOR SHELL (I) : 0.27100 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 67.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM CHLORIDE, MAGNESIUM CHLORIDE, REMARK 280 HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 24.69100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.50250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.91900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.50250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.69100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.91900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.69100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.91900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.50250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.91900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.69100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.50250 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 300 REMARK: THE OTHER HALF OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY: - REMARK 300 X+1, 1/2-Y+1, Z. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 49.38200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 101.75700 REMARK 350 BIOMT3 2 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 VAL A 108 REMARK 465 ASP A 109 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 GLU A 67 CG CD OE1 OE2 REMARK 470 HIS A 71 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 73 CG OD1 ND2 REMARK 470 LYS A 90 CG CD CE NZ 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 GLU A 26 13.47 58.06 REMARK 500 ALA A 32 -162.86 -106.08 REMARK 500 GLU A 67 -80.83 -61.82 REMARK 500 MET A 68 -52.65 -24.72 REMARK 500 HIS A 71 132.66 -36.89 REMARK 500 PRO A 72 -108.91 -48.22 REMARK 500 LEU A 105 35.35 -76.89 REMARK 500 REMARK 500 REMARK: NULL DBREF 1JBG A 1 109 UNP P71039 P71039_BACSU 1 109 SEQRES 1 A 109 MET LYS TYR GLN VAL LYS GLN VAL ALA GLU ILE SER GLY SEQRES 2 A 109 VAL SER ILE ARG THR LEU HIS HIS TYR ASP ASN ILE GLU SEQRES 3 A 109 LEU LEU ASN PRO SER ALA LEU THR ASP ALA GLY TYR ARG SEQRES 4 A 109 LEU TYR SER ASP ALA ASP LEU GLU ARG LEU GLN GLN ILE SEQRES 5 A 109 LEU PHE PHE LYS GLU ILE GLY PHE ARG LEU ASP GLU ILE SEQRES 6 A 109 LYS GLU MET LEU ASP HIS PRO ASN PHE ASP ARG LYS ALA SEQRES 7 A 109 ALA LEU GLN SER GLN LYS GLU ILE LEU MET LYS LYS LYS SEQRES 8 A 109 GLN ARG MET ASP GLU MET ILE GLN THR ILE ASP ARG THR SEQRES 9 A 109 LEU LEU SER VAL ASP FORMUL 2 HOH *16(H2 O) HELIX 1 1 VAL A 5 GLY A 13 1 9 HELIX 2 2 SER A 15 ILE A 25 1 11 HELIX 3 3 SER A 42 GLY A 59 1 18 HELIX 4 4 ARG A 61 HIS A 71 1 11 HELIX 5 5 ASP A 75 LEU A 105 1 31 SHEET 1 A 3 TYR A 3 GLN A 4 0 SHEET 2 A 3 ARG A 39 TYR A 41 -1 N TYR A 41 O TYR A 3 SHEET 3 A 3 ALA A 32 LEU A 33 -1 O ALA A 32 N LEU A 40 CRYST1 49.382 67.838 115.005 90.00 90.00 90.00 I 21 21 21 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 0.020250 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008695 0.00000