HEADER TRANSPORT PROTEIN 20-NOV-20 7B0K TITLE MEMBRANE PROTEIN STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DRUG/METABOLITE TRANSPORTER (DMT) SUPERFAMILY PERMEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MEMBRANE PROTEIN; COMPND 5 SYNONYM: EAMA FAMILY TRANSPORTER; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: ERS021280_00207, ERS409062_01153, GM533_00320, SOURCE 5 SAMEA104035127_01235, SAMEA104035134_01163, SAMEA104154639_01167, SOURCE 6 SAMEA104154682_01012, SAMEA2204024_01167, SAMEA3232645_00550, SOURCE 7 SAMEA3354337_01417, SAMEA3389964_01659, SAMEA3390019_01836, SOURCE 8 SAMEA3714202_00443; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CHOLINE TRANSPORTER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.BAERLAND,C.PEREZ REVDAT 1 16-MAR-22 7B0K 0 JRNL AUTH N.BARLAND,A.S.RUEFF,G.CEBRERO,C.A.J.HUTTER,M.A.SEEGER, JRNL AUTH 2 J.W.VEENING,C.PEREZ JRNL TITL MECHANISTIC BASIS OF CHOLINE IMPORT INVOLVED IN TEICHOIC JRNL TITL 2 ACIDS AND LIPOPOLYSACCHARIDE MODIFICATION. JRNL REF SCI ADV V. 8 M1122 2022 JRNL REFN ESSN 2375-2548 JRNL PMID 35235350 JRNL DOI 10.1126/SCIADV.ABM1122 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.BARLAND,A.S.RUEFF,G.CEBRERO,C.A.HUTTER,M.A.SEEGER, REMARK 1 AUTH 2 J.W.VEENING,C.PEREZ REMARK 1 TITL MECHANISTIC BASIS OF CHOLINE IMPORT INVOLVED IN TEICHOIC REMARK 1 TITL 2 ACIDS AND LIPOPOLYSACCHARIDE MODIFICATION REMARK 1 REF BIORXIV 2021 REMARK 1 REFN REMARK 1 DOI 10.1101/2021.09.14.460277 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 5147 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.311 REMARK 3 R VALUE (WORKING SET) : 0.309 REMARK 3 FREE R VALUE : 0.327 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 513 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 10.9600 - 5.8000 0.97 1340 143 0.2838 0.2959 REMARK 3 2 5.8000 - 4.7200 0.96 1281 145 0.3127 0.3487 REMARK 3 3 4.7200 - 4.1700 0.98 1295 143 0.3234 0.3144 REMARK 3 4 4.1700 - 3.8000 0.55 718 82 0.3653 0.4071 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) : 0.729 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 114.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 101.6 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 1984 REMARK 3 ANGLE : 0.564 2701 REMARK 3 CHIRALITY : 0.040 343 REMARK 3 PLANARITY : 0.004 314 REMARK 3 DIHEDRAL : 14.705 1137 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 7B0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292112398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5593 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.530 REMARK 200 RESOLUTION RANGE LOW (A) : 12.995 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 200 DATA REDUNDANCY : 3.259 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 37.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.52 REMARK 200 R MERGE FOR SHELL (I) : 0.57100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.320 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: OTHER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG 400, 50 MM HEPES PH 6.4, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 289K 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 64.45000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.45000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.72000 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 TOTAL BURIED SURFACE AREA: 360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 ASN A 5 REMARK 465 VAL A 57 REMARK 465 LYS A 58 REMARK 465 GLU A 59 REMARK 465 GLY A 60 REMARK 465 LYS A 61 REMARK 465 VAL A 62 REMARK 465 ARG A 63 REMARK 465 LEU A 64 REMARK 465 SER A 65 REMARK 465 ILE A 66 REMARK 465 PHE A 67 REMARK 465 LEU A 68 REMARK 465 ASN A 69 REMARK 465 GLU A 148 REMARK 465 GLN A 149 REMARK 465 VAL A 150 REMARK 465 ASN A 151 REMARK 465 SER A 152 REMARK 465 PHE A 153 REMARK 465 LEU A 204 REMARK 465 PHE A 205 REMARK 465 SER A 206 REMARK 465 HIS A 207 REMARK 465 GLN A 208 REMARK 465 SER A 209 REMARK 465 PHE A 210 REMARK 465 THR A 211 REMARK 465 ALA A 212 REMARK 465 VAL A 213 REMARK 465 ALA A 214 REMARK 465 ASN A 215 REMARK 465 GLU A 292 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 LEU A 91 -66.08 -91.19 REMARK 500 TYR A 96 16.95 -146.64 REMARK 500 ALA A 177 -85.23 -79.55 REMARK 500 GLU A 186 -35.16 -134.72 REMARK 500 LEU A 271 72.35 48.75 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7B0K A 1 292 UNP A0A0E7XN74_STREE DBREF2 7B0K A A0A0E7XN74 1 292 SEQRES 1 A 292 MET LYS SER LYS ASN GLY VAL PRO PHE GLY LEU LEU SER SEQRES 2 A 292 GLY ILE PHE TRP GLY LEU GLY LEU THR VAL SER ALA TYR SEQRES 3 A 292 ILE PHE SER ILE PHE THR ASP LEU SER PRO PHE VAL VAL SEQRES 4 A 292 ALA ALA THR HIS ASP PHE LEU SER ILE PHE ILE LEU LEU SEQRES 5 A 292 ALA PHE LEU LEU VAL LYS GLU GLY LYS VAL ARG LEU SER SEQRES 6 A 292 ILE PHE LEU ASN ILE ARG ASN VAL SER VAL ILE ILE GLY SEQRES 7 A 292 ALA LEU LEU ALA GLY PRO ILE GLY MET GLN ALA ASN LEU SEQRES 8 A 292 TYR ALA VAL LYS TYR ILE GLY SER SER LEU ALA SER SER SEQRES 9 A 292 VAL SER ALA ILE TYR PRO ALA ILE SER VAL LEU LEU ALA SEQRES 10 A 292 PHE PHE PHE LEU LYS HIS LYS ILE SER LYS ASN THR VAL SEQRES 11 A 292 PHE GLY ILE VAL LEU ILE ILE GLY GLY ILE ILE ALA GLN SEQRES 12 A 292 THR TYR LYS VAL GLU GLN VAL ASN SER PHE TYR ILE GLY SEQRES 13 A 292 ILE LEU CYS ALA LEU VAL CYS ALA ILE ALA TRP GLY SER SEQRES 14 A 292 GLU SER VAL LEU SER SER PHE ALA MET GLU SER GLU LEU SEQRES 15 A 292 SER GLU ILE GLU ALA LEU LEU ILE ARG GLN VAL THR SER SEQRES 16 A 292 PHE LEU SER TYR LEU VAL ILE VAL LEU PHE SER HIS GLN SEQRES 17 A 292 SER PHE THR ALA VAL ALA ASN GLY GLN LEU LEU GLY LEU SEQRES 18 A 292 MET ILE VAL PHE ALA ALA PHE ASP MET ILE SER TYR LEU SEQRES 19 A 292 ALA TYR TYR ILE ALA ILE ASN ARG LEU GLN PRO ALA LYS SEQRES 20 A 292 ALA THR GLY LEU ASN VAL SER TYR VAL VAL TRP THR VAL SEQRES 21 A 292 LEU PHE ALA VAL VAL PHE LEU GLY ALA PRO LEU ASP MET SEQRES 22 A 292 LEU THR ILE MET THR SER LEU VAL VAL ILE ALA GLY VAL SEQRES 23 A 292 TYR ILE ILE ILE LYS GLU HET CHT A 301 7 HETNAM CHT CHOLINE ION FORMUL 2 CHT C5 H14 N O 1+ HELIX 1 AA1 GLY A 6 SER A 29 1 24 HELIX 2 AA2 PHE A 37 ALA A 53 1 17 HELIX 3 AA3 PHE A 54 LEU A 56 5 3 HELIX 4 AA4 ARG A 71 LEU A 80 1 10 HELIX 5 AA5 GLY A 86 TYR A 92 1 7 HELIX 6 AA6 SER A 100 SER A 106 1 7 HELIX 7 AA7 ILE A 108 PHE A 118 1 11 HELIX 8 AA8 THR A 129 TYR A 145 1 17 HELIX 9 AA9 ILE A 155 ALA A 177 1 23 HELIX 10 AB1 GLU A 186 VAL A 203 1 18 HELIX 11 AB2 GLN A 217 LEU A 243 1 27 HELIX 12 AB3 GLN A 244 VAL A 253 1 10 HELIX 13 AB4 SER A 254 VAL A 256 5 3 HELIX 14 AB5 VAL A 257 PHE A 266 1 10 HELIX 15 AB6 ASP A 272 GLY A 285 1 14 HELIX 16 AB7 GLY A 285 ILE A 290 1 6 CRYST1 128.900 43.440 126.820 90.00 120.43 90.00 C 1 2 1 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 0.007758 0.000000 0.004557 0.00000 SCALE2 0.000000 0.023020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009145 0.00000