HEADER TRANSPORT PROTEIN 05-JUN-19 6P7F TITLE HUMAN ABCC6 NBD2 R1459D MUTANT IN APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1254-1503; COMPND 5 SYNONYM: ATP-BINDING CASSETTE SUB-FAMILY C MEMBER 6,ANTHRACYCLINE COMPND 6 RESISTANCE-ASSOCIATED PROTEIN,MULTI-SPECIFIC ORGANIC ANION COMPND 7 TRANSPORTER E,MOAT-E; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ABCC6, ARA, MRP6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ABCC6, NBD2, APO STATE, ATP-BINDING CASSETTE TRANSPORTER C6, KEYWDS 2 NUCLEOTIDE BINDING DOMAIN 2, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ZHENG,P.H.THIBODEAU REVDAT 2 11-OCT-23 6P7F 1 REMARK REVDAT 1 10-JUN-20 6P7F 0 JRNL AUTH A.ZHENG,P.H.THIBODEAU JRNL TITL STRUCTURES OF HUMAN ABCC6 NBD1 AND NBD2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.344 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.264 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.004 REMARK 3 FREE R VALUE TEST SET COUNT : 1026 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 44.4316 - 5.4491 1.00 1418 158 0.2654 0.2931 REMARK 3 2 5.4491 - 4.3262 0.99 1331 148 0.2333 0.2437 REMARK 3 3 4.3262 - 3.7797 1.00 1318 146 0.2275 0.2509 REMARK 3 4 3.7797 - 3.4343 0.99 1284 143 0.2616 0.2910 REMARK 3 5 3.4343 - 3.1882 1.00 1302 145 0.2750 0.3237 REMARK 3 6 3.1882 - 3.0003 1.00 1286 142 0.3019 0.3446 REMARK 3 7 3.0003 - 2.8500 1.00 1291 144 0.4082 0.4622 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) : 0.513 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.89 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 1918 REMARK 3 ANGLE : 1.129 2597 REMARK 3 CHIRALITY : 0.069 299 REMARK 3 PLANARITY : 0.006 335 REMARK 3 DIHEDRAL : 23.482 711 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 6P7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000241904. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10293 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 44.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 26.30 REMARK 200 R MERGE (I) : 0.18900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 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) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 28.17 REMARK 200 R MERGE FOR SHELL (I) : 2.08200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 6BZR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 1.6 M AMMONIUM REMARK 280 SULFATE, 10% DIOXANE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 42.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.67000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.67000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.67000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.67000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.67000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.67000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.67000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.00000 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 ALA A 1254 REMARK 465 ASP A 1397 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A1258 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PRO A1258 175.09 -53.15 REMARK 500 GLN A1390 -120.08 54.31 REMARK 500 THR A1429 -58.88 -136.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6BZR RELATED DB: PDB DBREF 6P7F A 1254 1503 UNP O95255 MRP6_HUMAN 1254 1503 SEQADV 6P7F ASP A 1459 UNP O95255 ARG 1459 ENGINEERED MUTATION SEQRES 1 A 250 ALA ALA GLN PRO PRO TRP PRO GLN GLY GLY GLN ILE GLU SEQRES 2 A 250 PHE ARG ASP PHE GLY LEU ARG TYR ARG PRO GLU LEU PRO SEQRES 3 A 250 LEU ALA VAL GLN GLY VAL SER PHE LYS ILE HIS ALA GLY SEQRES 4 A 250 GLU LYS VAL GLY ILE VAL GLY ARG THR GLY ALA GLY LYS SEQRES 5 A 250 SER SER LEU ALA SER GLY LEU LEU ARG LEU GLN GLU ALA SEQRES 6 A 250 ALA GLU GLY GLY ILE TRP ILE ASP GLY VAL PRO ILE ALA SEQRES 7 A 250 HIS VAL GLY LEU HIS THR LEU ARG SER ARG ILE SER ILE SEQRES 8 A 250 ILE PRO GLN ASP PRO ILE LEU PHE PRO GLY SER LEU ARG SEQRES 9 A 250 MET ASN LEU ASP LEU LEU GLN GLU HIS SER ASP GLU ALA SEQRES 10 A 250 ILE TRP ALA ALA LEU GLU THR VAL GLN LEU LYS ALA LEU SEQRES 11 A 250 VAL ALA SER LEU PRO GLY GLN LEU GLN TYR LYS CYS ALA SEQRES 12 A 250 ASP ARG GLY GLU ASP LEU SER VAL GLY GLN LYS GLN LEU SEQRES 13 A 250 LEU CYS LEU ALA ARG ALA LEU LEU ARG LYS THR GLN ILE SEQRES 14 A 250 LEU ILE LEU ASP GLU ALA THR ALA ALA VAL ASP PRO GLY SEQRES 15 A 250 THR GLU LEU GLN MET GLN ALA MET LEU GLY SER TRP PHE SEQRES 16 A 250 ALA GLN CYS THR VAL LEU LEU ILE ALA HIS ASP LEU ARG SEQRES 17 A 250 SER VAL MET ASP CYS ALA ARG VAL LEU VAL MET ASP LYS SEQRES 18 A 250 GLY GLN VAL ALA GLU SER GLY SER PRO ALA GLN LEU LEU SEQRES 19 A 250 ALA GLN LYS GLY LEU PHE TYR ARG LEU ALA GLN GLU SER SEQRES 20 A 250 GLY LEU VAL HET SO4 A1601 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- HELIX 1 AA1 GLY A 1304 LEU A 1313 1 10 HELIX 2 AA2 ALA A 1331 VAL A 1333 5 3 HELIX 3 AA3 GLY A 1334 ARG A 1341 1 8 HELIX 4 AA4 SER A 1355 ASP A 1361 1 7 HELIX 5 AA5 SER A 1367 VAL A 1378 1 12 HELIX 6 AA6 LEU A 1380 LEU A 1387 1 8 HELIX 7 AA7 GLY A 1389 TYR A 1393 5 5 HELIX 8 AA8 SER A 1403 LYS A 1419 1 17 HELIX 9 AA9 ASP A 1433 PHE A 1448 1 16 HELIX 10 AB1 SER A 1482 GLN A 1489 1 8 HELIX 11 AB2 GLY A 1491 SER A 1500 1 10 SHEET 1 AA1 4 VAL A1282 ILE A1289 0 SHEET 2 AA1 4 ILE A1265 LEU A1272 -1 N PHE A1267 O PHE A1287 SHEET 3 AA1 4 GLU A1320 ILE A1325 -1 O TRP A1324 N GLU A1266 SHEET 4 AA1 4 VAL A1328 PRO A1329 -1 O VAL A1328 N ILE A1325 SHEET 1 AA2 6 ILE A1342 ILE A1345 0 SHEET 2 AA2 6 ILE A1422 ASP A1426 1 O ILE A1424 N ILE A1345 SHEET 3 AA2 6 THR A1452 ILE A1456 1 O LEU A1454 N LEU A1423 SHEET 4 AA2 6 LYS A1294 GLY A1299 1 N ILE A1297 O LEU A1455 SHEET 5 AA2 6 ARG A1468 ASP A1473 1 O MET A1472 N VAL A1298 SHEET 6 AA2 6 GLN A1476 GLY A1481 -1 O GLY A1481 N VAL A1469 SITE 1 AC1 6 ARG A1300 GLY A1302 ALA A1303 GLY A1304 SITE 2 AC1 6 LYS A1305 SER A1306 CRYST1 99.340 99.340 84.000 90.00 90.00 90.00 P 41 21 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 0.010066 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011905 0.00000