HEADER TRANSPORT PROTEIN 08-JAN-19 6NLO TITLE HUMAN ABCC6 NBD1 H812A IN APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEOTIDE BINDING DOMAIN 1, RESIDUES 622-859; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ABCC6, NBD1, APO STATE, ATP-BINDING CASSETTE TRANSPORTER C6, KEYWDS 2 NUCLEOTIDE BINDING DOMAIN 1, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ZHENG,P.H.THIBODEAU REVDAT 2 11-OCT-23 6NLO 1 REMARK REVDAT 1 15-JAN-20 6NLO 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) : 39.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.476 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.978 REMARK 3 FREE R VALUE TEST SET COUNT : 544 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 39.5844 - 4.5228 1.00 1264 140 0.2125 0.2169 REMARK 3 2 4.5228 - 3.5906 1.00 1224 137 0.2110 0.2534 REMARK 3 3 3.5906 - 3.1369 1.00 1209 134 0.2500 0.3146 REMARK 3 4 3.1369 - 2.8502 1.00 1211 133 0.2986 0.3306 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) : 0.357 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.14 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 : 0.005 1733 REMARK 3 ANGLE : 0.766 2364 REMARK 3 CHIRALITY : 0.049 279 REMARK 3 PLANARITY : 0.006 305 REMARK 3 DIHEDRAL : 10.236 1027 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 6NLO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000238389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8-7.5 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 : 5467 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 39.581 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.41 REMARK 200 R MERGE (I) : 0.20400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3200 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.66 REMARK 200 R MERGE FOR SHELL (I) : 1.47400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 6BZS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1-2.4M AMMONIUM SULFATE 0.1M HEPES REMARK 280 PH 6.8-8.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 30.34000 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 15.17000 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 15.17000 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 30.34000 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 SER A 607 REMARK 465 ALA A 608 REMARK 465 GLY A 747 REMARK 465 GLU A 748 REMARK 465 GLN A 749 REMARK 465 ALA A 854 REMARK 465 ARG A 855 REMARK 465 GLN A 856 REMARK 465 PRO A 857 REMARK 465 GLY A 858 REMARK 465 ASP A 859 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 CYS A 628 -60.94 -108.71 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 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6BZR RELATED DB: PDB REMARK 900 NBD1 WT REMARK 900 RELATED ID: 6BZS RELATED DB: PDB REMARK 900 NBD2 WT DBREF 6NLO A 607 859 UNP O95255 MRP6_HUMAN 622 859 SEQADV 6NLO ALA A 812 UNP O95255 HIS 812 ENGINEERED MUTATION SEQADV 6NLO VAL A 848 UNP O95255 MET 848 VARIANT SEQRES 1 A 238 SER ALA ALA GLY LYS ASP CYS ILE THR ILE HIS SER ALA SEQRES 2 A 238 THR PHE ALA TRP SER GLN GLU SER PRO PRO CYS LEU HIS SEQRES 3 A 238 ARG ILE ASN LEU THR VAL PRO GLN GLY CYS LEU LEU ALA SEQRES 4 A 238 VAL VAL GLY PRO VAL GLY ALA GLY LYS SER SER LEU LEU SEQRES 5 A 238 SER ALA LEU LEU GLY GLU LEU SER LYS VAL GLU GLY PHE SEQRES 6 A 238 VAL SER ILE GLU GLY ALA VAL ALA TYR VAL PRO GLN GLU SEQRES 7 A 238 ALA TRP VAL GLN ASN THR SER VAL VAL GLU ASN VAL CYS SEQRES 8 A 238 PHE GLY GLN GLU LEU ASP PRO PRO TRP LEU GLU ARG VAL SEQRES 9 A 238 LEU GLU ALA CYS ALA LEU GLN PRO ASP VAL ASP SER PHE SEQRES 10 A 238 PRO GLU GLY ILE HIS THR SER ILE GLY GLU GLN GLY MET SEQRES 11 A 238 ASN LEU SER GLY GLY GLN LYS GLN ARG LEU SER LEU ALA SEQRES 12 A 238 ARG ALA VAL TYR ARG LYS ALA ALA VAL TYR LEU LEU ASP SEQRES 13 A 238 ASP PRO LEU ALA ALA LEU ASP ALA HIS VAL GLY GLN HIS SEQRES 14 A 238 VAL PHE ASN GLN VAL ILE GLY PRO GLY GLY LEU LEU GLN SEQRES 15 A 238 GLY THR THR ARG ILE LEU VAL THR ALA ALA LEU HIS ILE SEQRES 16 A 238 LEU PRO GLN ALA ASP TRP ILE ILE VAL LEU ALA ASN GLY SEQRES 17 A 238 ALA ILE ALA GLU MET GLY SER TYR GLN GLU LEU LEU GLN SEQRES 18 A 238 ARG LYS GLY ALA LEU VAL CYS LEU LEU ASP GLN ALA ARG SEQRES 19 A 238 GLN PRO GLY ASP HET SO4 A 901 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- HELIX 1 AA1 GLY A 668 LEU A 677 1 10 HELIX 2 AA2 SER A 706 PHE A 713 1 8 HELIX 3 AA3 ASP A 718 CYS A 729 1 12 HELIX 4 AA4 LEU A 731 PHE A 738 1 8 HELIX 5 AA5 GLU A 740 THR A 744 5 5 HELIX 6 AA6 SER A 754 ARG A 769 1 16 HELIX 7 AA7 ASP A 784 ILE A 796 1 13 HELIX 8 AA8 ILE A 816 ALA A 820 5 5 HELIX 9 AA9 GLN A 838 ARG A 843 1 6 HELIX 10 AB1 GLY A 845 GLN A 853 1 9 SHEET 1 AA1 3 LEU A 646 PRO A 654 0 SHEET 2 AA1 3 ASP A 627 ALA A 637 -1 N ALA A 634 O ILE A 649 SHEET 3 AA1 3 SER A 681 ILE A 689 -1 O SER A 688 N THR A 630 SHEET 1 AA2 6 VAL A 693 VAL A 696 0 SHEET 2 AA2 6 VAL A 773 ASP A 777 1 O VAL A 773 N ALA A 694 SHEET 3 AA2 6 THR A 806 VAL A 810 1 O ILE A 808 N LEU A 776 SHEET 4 AA2 6 LEU A 658 VAL A 662 1 N LEU A 659 O LEU A 809 SHEET 5 AA2 6 TRP A 822 ALA A 827 1 O ILE A 824 N ALA A 660 SHEET 6 AA2 6 ALA A 830 GLY A 835 -1 O ALA A 832 N VAL A 825 SITE 1 AC1 7 PRO A 664 VAL A 665 GLY A 666 ALA A 667 SITE 2 AC1 7 GLY A 668 LYS A 669 SER A 670 CRYST1 92.600 92.600 45.510 90.00 90.00 120.00 P 32 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 0.010799 0.006235 0.000000 0.00000 SCALE2 0.000000 0.012470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021973 0.00000