PDB Short entry for 4N7X HEADER TRANSPORT PROTEIN 16-OCT-13 4N7X TITLE THE E254A MUTANT OF THE SODIUM BILE ACID SYMPORTER FROM YERSINIA TITLE 2 FREDERIKSENII COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSPORTER, SODIUM/BILE ACID SYMPORTER FAMILY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA FREDERIKSENII; SOURCE 3 ORGANISM_TAXID: 29484; SOURCE 4 GENE: YFRED0001_28600; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS SLC10, SODIUM SYMPORT, BILE ACID, MEMBRANE PROTEIN, STRUCTURAL KEYWDS 2 GENOMICS, PSI-BIOLOGY, NEW YORK CONSORTIUM ON MEMBRANE PROTEIN KEYWDS 3 STRUCTURE, NYCOMPS, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHOU,E.J.LEVIN,M.ZHOU,NEW YORK CONSORTIUM ON MEMBRANE PROTEIN AUTHOR 2 STRUCTURE (NYCOMPS) REVDAT 3 28-FEB-24 4N7X 1 SEQADV REVDAT 2 22-JAN-14 4N7X 1 JRNL REVDAT 1 11-DEC-13 4N7X 0 JRNL AUTH X.ZHOU,E.J.LEVIN,Y.PAN,J.G.MCCOY,R.SHARMA,B.KLOSS,R.BRUNI, JRNL AUTH 2 M.QUICK,M.ZHOU JRNL TITL STRUCTURAL BASIS OF THE ALTERNATING-ACCESS MECHANISM IN A JRNL TITL 2 BILE ACID TRANSPORTER. JRNL REF NATURE V. 505 569 2013 JRNL REFN ISSN 0028-0836 JRNL PMID 24317697 JRNL DOI 10.1038/NATURE12811 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 12142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 609 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 45.7660 - 3.9679 1.00 3081 149 0.2257 0.2448 REMARK 3 2 3.9679 - 3.1497 1.00 2922 154 0.2054 0.2564 REMARK 3 3 3.1497 - 2.7516 1.00 2884 160 0.1927 0.2471 REMARK 3 4 2.7516 - 2.5000 0.92 2646 146 0.1715 0.2482 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.33 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 2348 REMARK 3 ANGLE : 0.790 3207 REMARK 3 CHIRALITY : 0.054 399 REMARK 3 PLANARITY : 0.005 384 REMARK 3 DIHEDRAL : 10.473 809 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 4N7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082864. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-12 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 : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99991 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12188 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 39% PEG 400, 100 MM TRIS-HCL, 100 MM REMARK 280 KCL, 20 MM MNCL2, 1-OLEOYL-RAC-GLYCEROL, PH 8.5, LIPID CUBIC REMARK 280 PHASE, TEMPERATURE 298K 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 27.08100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.76350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.92950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.76350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.08100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.92950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 VAL A 302 REMARK 465 LYS A 303 REMARK 465 LYS A 304 REMARK 465 ASP A 305 REMARK 465 GLN A 306 REMARK 465 GLU A 307 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 ASP A 152 106.81 -56.46 REMARK 500 VAL A 164 -67.90 -103.48 REMARK 500 PHE A 178 62.67 -113.94 REMARK 500 MET A 257 64.30 -115.21 REMARK 500 ASN A 259 88.23 -66.56 REMARK 500 PHE A 271 -121.59 -122.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N7W RELATED DB: PDB DBREF 4N7X A 1 307 UNP C4ST46 C4ST46_YERFR 1 307 SEQADV 4N7X ARG A -4 UNP C4ST46 EXPRESSION TAG SEQADV 4N7X ALA A -3 UNP C4ST46 EXPRESSION TAG SEQADV 4N7X HIS A -2 UNP C4ST46 EXPRESSION TAG SEQADV 4N7X HIS A -1 UNP C4ST46 EXPRESSION TAG SEQADV 4N7X HIS A 0 UNP C4ST46 EXPRESSION TAG SEQADV 4N7X ALA A 254 UNP C4ST46 GLU 254 ENGINEERED MUTATION SEQRES 1 A 312 ARG ALA HIS HIS HIS MET LEU VAL LYS ILE THR ARG LEU SEQRES 2 A 312 PHE PRO VAL TRP ALA LEU LEU LEU SER VAL ALA ALA TYR SEQRES 3 A 312 PHE ARG PRO THR THR PHE THR GLY ILE GLY PRO TYR VAL SEQRES 4 A 312 GLY PRO LEU LEU MET LEU ILE MET PHE ALA MET GLY VAL SEQRES 5 A 312 THR LEU ARG LEU ASP ASP PHE LYS ARG VAL LEU SER ARG SEQRES 6 A 312 PRO ALA PRO VAL ALA ALA ALA THR PHE LEU HIS TYR LEU SEQRES 7 A 312 ILE MET PRO LEU THR ALA TRP ILE LEU ALA MET LEU PHE SEQRES 8 A 312 ARG MET PRO PRO ASP LEU SER ALA GLY MET VAL LEU VAL SEQRES 9 A 312 GLY SER VAL ALA SER GLY THR ALA SER ASN VAL MET ILE SEQRES 10 A 312 TYR LEU ALA LYS GLY ASP VAL ALA LEU SER VAL THR ILE SEQRES 11 A 312 SER ALA VAL SER THR LEU VAL GLY VAL PHE ALA THR PRO SEQRES 12 A 312 LEU LEU THR ARG LEU TYR VAL ASP ALA THR ILE SER VAL SEQRES 13 A 312 ASP VAL VAL GLY MET LEU LYS SER ILE LEU GLN ILE VAL SEQRES 14 A 312 VAL ILE PRO ILE THR ALA GLY LEU VAL ILE HIS HIS THR SEQRES 15 A 312 PHE THR LYS THR VAL LYS ARG ILE GLU PRO TYR LEU PRO SEQRES 16 A 312 ALA MET SER MET VAL CYS ILE LEU ALA ILE ILE SER ALA SEQRES 17 A 312 VAL VAL ALA GLY SER GLN SER HIS ILE ALA SER VAL GLY SEQRES 18 A 312 PHE VAL VAL ILE ILE ALA VAL ILE LEU HIS ASN GLY ILE SEQRES 19 A 312 GLY LEU LEU SER GLY TYR TRP GLY GLY LYS LEU PHE GLY SEQRES 20 A 312 PHE ASP GLU SER THR CYS ARG THR LEU ALA ILE ALA VAL SEQRES 21 A 312 GLY MET GLN ASN SER GLY LEU ALA ALA THR LEU GLY LYS SEQRES 22 A 312 ILE TYR PHE SER PRO LEU ALA ALA LEU PRO GLY ALA LEU SEQRES 23 A 312 PHE SER VAL TRP HIS ASN LEU SER GLY SER LEU LEU ALA SEQRES 24 A 312 GLY TYR TRP SER GLY LYS PRO VAL LYS LYS ASP GLN GLU FORMUL 2 HOH *14(H2 O) HELIX 1 1 ARG A -4 LEU A 8 1 13 HELIX 2 2 LEU A 8 ARG A 23 1 16 HELIX 3 3 PRO A 24 PRO A 32 5 9 HELIX 4 4 TYR A 33 THR A 48 1 16 HELIX 5 5 ARG A 50 ARG A 60 1 11 HELIX 6 6 PRO A 61 ILE A 74 1 14 HELIX 7 7 ILE A 74 PHE A 86 1 13 HELIX 8 8 PRO A 89 SER A 101 1 13 HELIX 9 9 THR A 106 ALA A 115 1 10 HELIX 10 10 ASP A 118 ASP A 146 1 29 HELIX 11 11 ASP A 152 VAL A 164 1 13 HELIX 12 12 VAL A 164 PHE A 178 1 15 HELIX 13 13 PHE A 178 GLU A 186 1 9 HELIX 14 14 TYR A 188 SER A 208 1 21 HELIX 15 15 SER A 208 ALA A 213 1 6 HELIX 16 16 PHE A 217 PHE A 241 1 25 HELIX 17 17 ASP A 244 MET A 257 1 14 HELIX 18 18 ASN A 259 PHE A 271 1 13 HELIX 19 19 SER A 272 ALA A 275 5 4 HELIX 20 20 ALA A 276 SER A 298 1 23 CRYST1 54.162 73.859 85.527 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 0.018463 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011692 0.00000