HEADER TRANSPORT PROTEIN 09-JAN-18 6FFV OBSLTE 31-JAN-24 6FFV 8C7P TITLE THE CRYSTAL STRUCTURE OF BTUM COBALAMIN TRANSPORTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: BTUM; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: OCTA-HIS-TAG AT C-TERMINUS; GLY AT THE 2ND POSITION IS COMPND 6 A CLONING ARTEFACT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THIOBACILLUS DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 36861; SOURCE 4 GENE: TBD_2719; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COBALAMIN, S-COMPONENT, BTUM, ECF TRANSPORTER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.REMPEL,E.COLUCCI,J.W.DE GIER,A.GUSKOV,D.J.SLOTBOOM REVDAT 6 31-JAN-24 6FFV 1 OBSLTE HETSYN REVDAT 5 29-JUL-20 6FFV 1 COMPND REMARK HETNAM SITE REVDAT 4 20-NOV-19 6FFV 1 LINK REVDAT 3 19-SEP-18 6FFV 1 REMARK REVDAT 2 15-AUG-18 6FFV 1 JRNL REVDAT 1 08-AUG-18 6FFV 0 JRNL AUTH S.REMPEL,E.COLUCCI,J.W.DE GIER,A.GUSKOV,D.J.SLOTBOOM JRNL TITL CYSTEINE-MEDIATED DECYANATION OF VITAMIN B12 BY THE JRNL TITL 2 PREDICTED MEMBRANE TRANSPORTER BTUM. JRNL REF NAT COMMUN V. 9 3038 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30072686 JRNL DOI 10.1038/S41467-018-05441-9 REMARK 2 REMARK 2 RESOLUTION. 2.01 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 55077 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2742 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 43.7804 - 5.4526 1.00 2649 141 0.2072 0.2518 REMARK 3 2 5.4526 - 4.3292 1.00 2668 142 0.1983 0.2621 REMARK 3 3 4.3292 - 3.7823 1.00 2633 139 0.1799 0.1938 REMARK 3 4 3.7823 - 3.4366 1.00 2693 138 0.1883 0.2130 REMARK 3 5 3.4366 - 3.1904 1.00 2650 140 0.1835 0.1737 REMARK 3 6 3.1904 - 3.0023 1.00 2652 138 0.1816 0.2053 REMARK 3 7 3.0023 - 2.8520 1.00 2661 135 0.1726 0.2307 REMARK 3 8 2.8520 - 2.7279 1.00 2638 137 0.1758 0.2015 REMARK 3 9 2.7279 - 2.6229 1.00 2665 139 0.1670 0.2376 REMARK 3 10 2.6229 - 2.5324 1.00 2645 137 0.1839 0.1791 REMARK 3 11 2.5324 - 2.4532 1.00 2694 138 0.1977 0.2349 REMARK 3 12 2.4532 - 2.3831 1.00 2625 134 0.2053 0.2572 REMARK 3 13 2.3831 - 2.3203 1.00 2670 145 0.2487 0.3020 REMARK 3 14 2.3203 - 2.2637 0.89 2317 122 0.3194 0.3755 REMARK 3 15 2.2637 - 2.2123 0.83 2211 118 0.5051 0.5476 REMARK 3 16 2.2123 - 2.1652 1.00 2629 137 0.3120 0.3642 REMARK 3 17 2.1652 - 2.1219 1.00 2655 141 0.3267 0.3148 REMARK 3 18 2.1219 - 2.0818 1.00 2621 135 0.3414 0.3834 REMARK 3 19 2.0818 - 2.0447 1.00 2689 142 0.3623 0.3557 REMARK 3 20 2.0447 - 2.0100 1.00 2670 144 0.4260 0.3821 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.770 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 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 : 0.009 1887 REMARK 3 ANGLE : 1.815 2548 REMARK 3 CHIRALITY : 0.256 283 REMARK 3 PLANARITY : 0.009 285 REMARK 3 DIHEDRAL : 22.208 1035 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 207) REMARK 3 ORIGIN FOR THE GROUP (A): 19.9326 33.8842 13.3856 REMARK 3 T TENSOR REMARK 3 T11: 0.5988 T22: 0.4240 REMARK 3 T33: 0.4712 T12: 0.0858 REMARK 3 T13: -0.0292 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 3.0300 L22: 3.5766 REMARK 3 L33: 3.2898 L12: -1.3947 REMARK 3 L13: -1.2870 L23: 1.4935 REMARK 3 S TENSOR REMARK 3 S11: -0.2739 S12: -0.0427 S13: -0.2214 REMARK 3 S21: 0.4980 S22: 0.1570 S23: 0.1777 REMARK 3 S31: 0.1925 S32: 0.0110 S33: 0.1336 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 6FFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200007888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-17; 12-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SLS; ESRF REMARK 200 BEAMLINE : X06SA; ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1; 1.4 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; CCD REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M; ADSC REMARK 200 QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55077 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 43.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM TRIS PH 8.5 AND 25% TO 30% (V/V) REMARK 280 PEG400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.63667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.27333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.27333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.63667 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: 6590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 33.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 428 LIES ON A SPECIAL POSITION. 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 ASP A 186 REMARK 465 GLY A 187 REMARK 465 ASP A 188 REMARK 465 PRO A 189 REMARK 465 ARG A 190 REMARK 465 THR A 191 REMARK 465 LEU A 192 REMARK 465 MET A 193 REMARK 465 GLY A 194 REMARK 465 THR A 195 REMARK 465 ARG A 196 REMARK 465 ARG A 197 REMARK 465 GLU A 198 DBREF 6FFV A 3 199 UNP Q3SFD8 Q3SFD8_THIDA 2 198 SEQADV 6FFV MET A 1 UNP Q3SFD8 INITIATING METHIONINE SEQADV 6FFV GLY A 2 UNP Q3SFD8 CLONING ARTIFACT SEQADV 6FFV HIS A 200 UNP Q3SFD8 EXPRESSION TAG SEQADV 6FFV HIS A 201 UNP Q3SFD8 EXPRESSION TAG SEQADV 6FFV HIS A 202 UNP Q3SFD8 EXPRESSION TAG SEQADV 6FFV HIS A 203 UNP Q3SFD8 EXPRESSION TAG SEQADV 6FFV HIS A 204 UNP Q3SFD8 EXPRESSION TAG SEQADV 6FFV HIS A 205 UNP Q3SFD8 EXPRESSION TAG SEQADV 6FFV HIS A 206 UNP Q3SFD8 EXPRESSION TAG SEQADV 6FFV HIS A 207 UNP Q3SFD8 EXPRESSION TAG SEQRES 1 A 207 MET GLY LEU ASN LEU THR ARG ARG GLN GLN ILE ALA ILE SEQRES 2 A 207 GLY PHE VAL LEU VAL LEU MET MET LEU LEU THR ARG SER SEQRES 3 A 207 HIS HIS TRP ALA SER ILE HIS SER LEU PRO ASP ALA SER SEQRES 4 A 207 TRP ALA ILE PHE PHE LEU LEU GLY VAL TYR VAL ARG ALA SEQRES 5 A 207 LEU TRP VAL VAL PRO ALA LEU ILE ALA ALA SER VAL VAL SEQRES 6 A 207 ILE ASP TYR VAL ALA ILE THR TRP GLY GLY VAL SER ASP SEQRES 7 A 207 PHE CYS VAL SER PRO ALA TYR TRP LEU LEU ILE PRO ALA SEQRES 8 A 207 TYR LEU ALA LEU PHE ALA GLY GLY ARG PHE TYR ALA ARG SEQRES 9 A 207 GLY HIS SER LEU SER LEU LEU GLY LEU PHE ARG LEU ALA SEQRES 10 A 207 GLY VAL ALA LEU ALA VAL VAL ALA VAL ALA GLN LEU LEU SEQRES 11 A 207 THR THR GLY GLY PHE TYR PHE TYR SER GLY ARG PHE ALA SEQRES 12 A 207 ASP PRO THR LEU ALA GLY LEU VAL LEU ARG LEU GLU LYS SEQRES 13 A 207 TYR PHE PRO PRO MET LEU GLY THR PHE ALA LEU TYR VAL SEQRES 14 A 207 GLY LEU ALA ALA THR VAL HIS VAL ALA LEU ALA ALA VAL SEQRES 15 A 207 PHE ARG ARG ASP GLY ASP PRO ARG THR LEU MET GLY THR SEQRES 16 A 207 ARG ARG GLU ARG HIS HIS HIS HIS HIS HIS HIS HIS HET B12 A 301 91 HET PG4 A 302 13 HET PG4 A 303 13 HET PG4 A 304 13 HET PG4 A 305 13 HET PG4 A 306 13 HET BNG A 307 21 HET BNG A 308 21 HET BNG A 309 21 HET PEG A 310 7 HET PEG A 311 7 HET PEG A 312 7 HET PEG A 313 7 HET PEG A 314 7 HET PEG A 315 7 HET PEG A 316 7 HET PGE A 317 10 HETNAM B12 COBALAMIN HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM BNG NONYL BETA-D-GLUCOPYRANOSIDE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETSYN BNG BETA-NONYLGLUCOSIDE; NONYL BETA-D-GLUCOSIDE; NONYL D- HETSYN 2 BNG GLUCOSIDE; NONYL GLUCOSIDE FORMUL 2 B12 C62 H89 CO N13 O14 P 2+ FORMUL 3 PG4 5(C8 H18 O5) FORMUL 8 BNG 3(C15 H30 O6) FORMUL 11 PEG 7(C4 H10 O3) FORMUL 18 PGE C6 H14 O4 FORMUL 19 HOH *28(H2 O) HELIX 1 AA1 THR A 6 SER A 26 1 21 HELIX 2 AA2 SER A 26 SER A 34 1 9 HELIX 3 AA3 ALA A 38 VAL A 50 1 13 HELIX 4 AA4 TRP A 54 TRP A 73 1 20 HELIX 5 AA5 ALA A 84 TRP A 86 5 3 HELIX 6 AA6 LEU A 87 GLY A 105 1 19 HELIX 7 AA7 SER A 109 SER A 139 1 31 HELIX 8 AA8 THR A 146 PHE A 183 1 38 HELIX 9 AA9 HIS A 202 HIS A 206 5 5 CRYST1 87.540 87.540 97.910 90.00 90.00 120.00 P 31 2 1 6 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 0.011423 0.006595 0.000000 0.00000 SCALE2 0.000000 0.013191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010213 0.00000