HEADER LIPID BINDING PROTEIN 23-JUL-18 6E5T TITLE CRYSTAL STRUCTURE OF HUMAN CELLULAR RETINOL BINDING PROTEIN 1 IN TITLE 2 COMPLEX WITH ABNORMAL-CANNABIDIORCIN (ABN-CBDO) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN,CRBP,CELLULAR RETINOL- COMPND 5 BINDING PROTEIN I,CRBP-I; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RBP1, CRBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS VITAMIN A, RETINOL, ABN-CBDO, ABNORMAL CANNABIDIORCIN, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.A.SILVAROLI,S.HORWITZ,S.BANERJEE,P.D.KISER,M.GOLCZAK REVDAT 4 11-OCT-23 6E5T 1 REMARK REVDAT 3 11-DEC-19 6E5T 1 REMARK REVDAT 2 28-AUG-19 6E5T 1 JRNL REVDAT 1 13-FEB-19 6E5T 0 JRNL AUTH J.A.SILVAROLI,M.A.K.WIDJAJA-ADHI,T.TRISCHMAN,S.CHELSTOWSKA, JRNL AUTH 2 S.HORWITZ,S.BANERJEE,P.D.KISER,W.S.BLANER,M.GOLCZAK JRNL TITL ABNORMAL CANNABIDIOL MODULATES VITAMIN A METABOLISM BY JRNL TITL 2 ACTING AS A COMPETITIVE INHIBITOR OF CRBP1. JRNL REF ACS CHEM.BIOL. V. 14 434 2019 JRNL REFN ESSN 1554-8937 JRNL PMID 30721022 JRNL DOI 10.1021/ACSCHEMBIO.8B01070 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 20856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1077 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 34.5949 - 3.0994 0.99 2613 149 0.1466 0.1928 REMARK 3 2 3.0994 - 2.4603 1.00 2513 150 0.1717 0.2293 REMARK 3 3 2.4603 - 2.1494 0.98 2457 127 0.1677 0.2073 REMARK 3 4 2.1494 - 1.9529 1.00 2473 132 0.1775 0.2606 REMARK 3 5 1.9529 - 1.8129 1.00 2479 130 0.1977 0.2308 REMARK 3 6 1.8129 - 1.7060 0.99 2453 114 0.2330 0.2696 REMARK 3 7 1.7060 - 1.6206 0.96 2353 140 0.2683 0.3104 REMARK 3 8 1.6206 - 1.5500 0.99 2438 135 0.2937 0.3259 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.460 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 1254 REMARK 3 ANGLE : 1.042 1696 REMARK 3 CHIRALITY : 0.065 176 REMARK 3 PLANARITY : 0.006 218 REMARK 3 DIHEDRAL : 14.460 758 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 16.8424 42.2397 102.3174 REMARK 3 T TENSOR REMARK 3 T11: 0.1476 T22: 0.1375 REMARK 3 T33: 0.1358 T12: -0.0341 REMARK 3 T13: -0.0335 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.8671 L22: 1.2867 REMARK 3 L33: 1.3427 L12: 0.2180 REMARK 3 L13: -0.4465 L23: -0.2529 REMARK 3 S TENSOR REMARK 3 S11: 0.0878 S12: 0.0966 S13: -0.1501 REMARK 3 S21: 0.1072 S22: -0.0741 S23: -0.0509 REMARK 3 S31: 0.0508 S32: -0.0485 S33: -0.0003 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 6E5T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20911 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 46.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09200 REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.83000 REMARK 200 FOR SHELL : 2.900 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: 5H8T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BISTRIS, PH 5.5, 25% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.65950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.03950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.36950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.03950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.65950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.36950 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 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 HIS A 140 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 457 O HOH A 514 1.99 REMARK 500 O HOH A 531 O HOH A 537 2.01 REMARK 500 O HOH A 366 O HOH A 456 2.03 REMARK 500 O HOH A 536 O HOH A 539 2.13 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 ARG A 58 149.70 -173.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 539 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 540 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 541 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 542 DISTANCE = 6.47 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HVJ A 201 DBREF 6E5T A 1 134 UNP P09455 RET1_HUMAN 2 135 SEQADV 6E5T HIS A 135 UNP P09455 EXPRESSION TAG SEQADV 6E5T HIS A 136 UNP P09455 EXPRESSION TAG SEQADV 6E5T HIS A 137 UNP P09455 EXPRESSION TAG SEQADV 6E5T HIS A 138 UNP P09455 EXPRESSION TAG SEQADV 6E5T HIS A 139 UNP P09455 EXPRESSION TAG SEQADV 6E5T HIS A 140 UNP P09455 EXPRESSION TAG SEQRES 1 A 140 PRO VAL ASP PHE THR GLY TYR TRP LYS MET LEU VAL ASN SEQRES 2 A 140 GLU ASN PHE GLU GLU TYR LEU ARG ALA LEU ASP VAL ASN SEQRES 3 A 140 VAL ALA LEU ARG LYS ILE ALA ASN LEU LEU LYS PRO ASP SEQRES 4 A 140 LYS GLU ILE VAL GLN ASP GLY ASP HIS MET ILE ILE ARG SEQRES 5 A 140 THR LEU SER THR PHE ARG ASN TYR ILE MET ASP PHE GLN SEQRES 6 A 140 VAL GLY LYS GLU PHE GLU GLU ASP LEU THR GLY ILE ASP SEQRES 7 A 140 ASP ARG LYS CYS MET THR THR VAL SER TRP ASP GLY ASP SEQRES 8 A 140 LYS LEU GLN CYS VAL GLN LYS GLY GLU LYS GLU GLY ARG SEQRES 9 A 140 GLY TRP THR GLN TRP ILE GLU GLY ASP GLU LEU HIS LEU SEQRES 10 A 140 GLU MET ARG VAL GLU GLY VAL VAL CYS LYS GLN VAL PHE SEQRES 11 A 140 LYS LYS VAL GLN HIS HIS HIS HIS HIS HIS HET HVJ A 201 41 HETNAM HVJ (1'R,2'R)-5',6-DIMETHYL-2'-(PROP-1-EN-2-YL)-1',2',3', HETNAM 2 HVJ 4'-TETRAHYDRO[1,1'-BIPHENYL]-2,4-DIOL FORMUL 2 HVJ C17 H22 O2 FORMUL 3 HOH *242(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASN A 26 ASN A 34 1 9 HELIX 3 AA3 LEU A 74 ASP A 79 1 6 SHEET 1 AA110 TYR A 60 GLN A 65 0 SHEET 2 AA110 HIS A 48 LEU A 54 -1 N MET A 49 O PHE A 64 SHEET 3 AA110 ASP A 39 ASP A 45 -1 N GLU A 41 O ARG A 52 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O LYS A 40 SHEET 5 AA110 VAL A 124 VAL A 133 -1 O VAL A 129 N LEU A 11 SHEET 6 AA110 GLU A 114 VAL A 121 -1 N LEU A 117 O GLN A 128 SHEET 7 AA110 GLY A 105 GLU A 111 -1 N GLY A 105 O ARG A 120 SHEET 8 AA110 LYS A 92 LYS A 98 -1 N CYS A 95 O TRP A 106 SHEET 9 AA110 LYS A 81 ASP A 89 -1 N SER A 87 O GLN A 94 SHEET 10 AA110 PHE A 70 ASP A 73 -1 N PHE A 70 O THR A 84 SITE 1 AC1 9 MET A 10 PHE A 16 ALA A 33 PRO A 38 SITE 2 AC1 9 SER A 55 ARG A 58 TYR A 60 GLN A 128 SITE 3 AC1 9 HOH A 392 CRYST1 37.319 40.739 92.079 90.00 90.00 90.00 P 21 21 21 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 0.026796 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010860 0.00000