HEADER TRANSPORT PROTEIN 06-DEC-19 6LH1 TITLE CRYSTAL STRUCTURE OF A CYSTEINE-PAIR MUTANT (Y113C-P190C) OF A TITLE 2 BACTERIAL BILE ACID TRANSPORTER TRAPPED IN AN OUTWARD-FACING TITLE 3 CONFORMATION 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: NCTC11470_02445; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BILE ACID TRANSPORTER, ASBT, NTCP, SLC10, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,Y.LYU,Y.JI,Z.SUN,X.ZHOU REVDAT 3 22-NOV-23 6LH1 1 REMARK REVDAT 2 13-JAN-21 6LH1 1 JRNL REVDAT 1 09-DEC-20 6LH1 0 JRNL AUTH X.WANG,Y.LYU,Y.JI,Z.SUN,X.ZHOU JRNL TITL AN ENGINEERED DISULFIDE BRIDGE TRAPS AND VALIDATES AN JRNL TITL 2 OUTWARD-FACING CONFORMATION IN A BILE ACID TRANSPORTER. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 77 108 2021 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 33404530 JRNL DOI 10.1107/S205979832001517X REMARK 2 REMARK 2 RESOLUTION. 2.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 7548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 360 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 48.2790 - 4.1251 0.96 2504 119 0.2106 0.2699 REMARK 3 2 4.1251 - 3.2745 0.93 2268 126 0.2307 0.2364 REMARK 3 3 3.2745 - 2.8610 0.99 2416 115 0.2710 0.3057 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.64 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6LH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97852 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7621 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.851 REMARK 200 RESOLUTION RANGE LOW (A) : 48.279 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.72400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4N7X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4H2PO4, 0.1 M (NH4)2SO4, 0.1 M REMARK 280 NA+-CITRATE PH 5.0, 34% PEG 400, 4% 1,3-BUTANEDIOL, LIPIDIC REMARK 280 CUBIC PHASE, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 21.68300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.50250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 96.55700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.68300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.50250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 96.55700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.68300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.50250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.55700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.68300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.50250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 96.55700 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 TOTAL BURIED SURFACE AREA: 460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 ARG A -4 REMARK 465 ALA A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 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 ARG A 60 78.51 -119.74 REMARK 500 PHE A 271 -75.63 -131.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7CYG RELATED DB: PDB REMARK 900 7CYG CONTAINS THE SAME MUTATIOS OF THE SAME PROTEIN IN AN INWARD- REMARK 900 FACING CONFORMATION. REMARK 900 RELATED ID: 7CYK RELATED DB: PDB REMARK 900 7CYK CONTAINS DIFFERENT MUTATIOS OF THE SAME PROTEIN IN AN INWARD- REMARK 900 FACING CONFORMATION. DBREF1 6LH1 A 1 307 UNP A0A380PV03_YERFR DBREF2 6LH1 A A0A380PV03 1 307 SEQADV 6LH1 ARG A -4 UNP A0A380PV0 EXPRESSION TAG SEQADV 6LH1 ALA A -3 UNP A0A380PV0 EXPRESSION TAG SEQADV 6LH1 HIS A -2 UNP A0A380PV0 EXPRESSION TAG SEQADV 6LH1 HIS A -1 UNP A0A380PV0 EXPRESSION TAG SEQADV 6LH1 HIS A 0 UNP A0A380PV0 EXPRESSION TAG SEQADV 6LH1 CYS A 113 UNP A0A380PV0 TYR 113 ENGINEERED MUTATION SEQADV 6LH1 CYS A 190 UNP A0A380PV0 PRO 190 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 CYS 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 CYS 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 GLU 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 HET CIT A 401 13 HET A6L A 402 25 HET A6L A 403 25 HETNAM CIT CITRIC ACID HETNAM A6L 2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETSYN A6L MONOOLEIN FORMUL 2 CIT C6 H8 O7 FORMUL 3 A6L 2(C21 H40 O4) FORMUL 5 HOH *16(H2 O) HELIX 1 AA1 LEU A 8 ARG A 23 1 16 HELIX 2 AA2 PRO A 24 PRO A 32 5 9 HELIX 3 AA3 TYR A 33 THR A 48 1 16 HELIX 4 AA4 ARG A 50 ARG A 60 1 11 HELIX 5 AA5 PRO A 61 PHE A 86 1 26 HELIX 6 AA6 PRO A 89 VAL A 102 1 14 HELIX 7 AA7 THR A 106 ALA A 115 1 10 HELIX 8 AA8 ASP A 118 ASP A 146 1 29 HELIX 9 AA9 ASP A 152 VAL A 164 1 13 HELIX 10 AB1 VAL A 164 PHE A 178 1 15 HELIX 11 AB2 PHE A 178 SER A 208 1 31 HELIX 12 AB3 SER A 208 PHE A 241 1 34 HELIX 13 AB4 ASP A 244 MET A 257 1 14 HELIX 14 AB5 ASN A 259 PHE A 271 1 13 HELIX 15 AB6 SER A 272 ALA A 275 5 4 HELIX 16 AB7 ALA A 276 LYS A 300 1 25 SSBOND 1 CYS A 113 CYS A 190 1555 1555 2.03 CRYST1 43.366 77.005 193.114 90.00 90.00 90.00 I 2 2 2 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 0.023060 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005178 0.00000