HEADER RETINOL BINDING PROTEIN 07-APR-25 9O3M TITLE K40F MUTANT OF HCRBPII BOUND TO FENTANYL COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN II,CRBP-II; COMPND 5 ENGINEERED: YES; COMPND 6 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: RBP2, CRBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN CELLULAR RETINOL BINDING PROTEIN II, HCRBPII, FENTANYL, OPIOID, KEYWDS 2 ENGINEERED PROTEIN, RETINOL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.BINGHAM,J.H.GEIGER REVDAT 1 22-APR-26 9O3M 0 JRNL AUTH C.BINGHAM,J.H.GEIGER JRNL TITL K40F MUTANT OF HCRBPII BOUND TO FENTANYL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6-3549 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 39285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.85 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 2288 REMARK 3 ANGLE : 0.798 3087 REMARK 3 CHIRALITY : 0.083 330 REMARK 3 PLANARITY : 0.004 397 REMARK 3 DIHEDRAL : 20.257 1335 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 9O3M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-25. REMARK 100 THE DEPOSITION ID IS D_1000294797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39316 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 29.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, AMMONIUM ACETATE, SODIUM REMARK 280 ACETATE, PH 4.0 - 4.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 LYS B 31 CG CD CE NZ REMARK 470 ARG B 58 CG CD NE CZ NH1 NH2 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 ASP A 24 30.45 71.44 REMARK 500 SER A 76 -18.20 77.00 REMARK 500 LEU A 77 -106.76 -96.21 REMARK 500 LYS B 75 -119.40 60.48 REMARK 500 LEU B 77 -92.10 -70.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 9O3M A 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 9O3M B 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 9O3M PHE A 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 9O3M PHE B 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQRES 1 A 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 A 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 133 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 A 133 PHE VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 A 133 THR THR SER THR PHE ARG ASN TYR ASP VAL ASP PHE THR SEQRES 6 A 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 A 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 A 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 A 133 GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 A 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 A 133 LYS LYS LYS SEQRES 1 B 133 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 B 133 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 B 133 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 B 133 PHE VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 B 133 THR THR SER THR PHE ARG ASN TYR ASP VAL ASP PHE THR SEQRES 6 B 133 VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SER LEU ASP SEQRES 7 B 133 ASN ARG HIS VAL LYS ALA LEU VAL THR TRP GLU GLY ASP SEQRES 8 B 133 VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS GLU ASN ARG SEQRES 9 B 133 GLY TRP LYS GLN TRP ILE GLU GLY ASP LYS LEU TYR LEU SEQRES 10 B 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 B 133 LYS LYS LYS HET ACT A 301 4 HET GOL A 302 6 HET GOL A 303 6 HET 7V7 A 304 53 HET GOL A 305 6 HET GOL B 201 6 HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM 7V7 N-PHENYL-N-[1-(2-PHENYLETHYL)PIPERIDIN-4-YL]PROPANAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 GOL 4(C3 H8 O3) FORMUL 6 7V7 C22 H28 N2 O FORMUL 9 HOH *120(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASP A 26 LEU A 36 1 11 HELIX 3 AA3 ASN B 15 LEU B 23 1 9 HELIX 4 AA4 ASP B 26 VAL B 34 1 9 SHEET 1 AA110 ASN A 59 THR A 65 0 SHEET 2 AA110 ASN A 48 THR A 54 -1 N PHE A 49 O PHE A 64 SHEET 3 AA110 THR A 39 ASP A 45 -1 N ASP A 43 O LYS A 50 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O PHE A 40 SHEET 5 AA110 GLN A 124 LYS A 132 -1 O LYS A 131 N GLU A 9 SHEET 6 AA110 LYS A 114 CYS A 121 -1 N LEU A 117 O GLN A 128 SHEET 7 AA110 GLY A 105 GLU A 111 -1 N TRP A 109 O TYR A 116 SHEET 8 AA110 VAL A 92 LYS A 98 -1 N LEU A 93 O GLN A 108 SHEET 9 AA110 HIS A 81 GLU A 89 -1 N THR A 87 O VAL A 94 SHEET 10 AA110 PHE A 70 TYR A 73 -1 N GLU A 72 O VAL A 82 SHEET 1 AA210 ASN B 59 THR B 65 0 SHEET 2 AA210 ASN B 48 THR B 54 -1 N PHE B 49 O PHE B 64 SHEET 3 AA210 THR B 39 ASP B 45 -1 N VAL B 41 O LYS B 52 SHEET 4 AA210 GLY B 6 GLU B 14 -1 N GLY B 6 O ILE B 42 SHEET 5 AA210 GLN B 124 LYS B 132 -1 O VAL B 129 N GLU B 11 SHEET 6 AA210 LYS B 114 CYS B 121 -1 N LEU B 117 O GLN B 128 SHEET 7 AA210 GLY B 105 GLU B 111 -1 N TRP B 109 O TYR B 116 SHEET 8 AA210 VAL B 92 LYS B 98 -1 N CYS B 95 O TRP B 106 SHEET 9 AA210 HIS B 81 GLU B 89 -1 N THR B 87 O VAL B 94 SHEET 10 AA210 PHE B 70 TYR B 73 -1 N PHE B 70 O ALA B 84 CRYST1 29.965 35.685 63.731 91.03 86.94 67.41 P 1 2 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 0.033372 -0.013885 -0.002366 0.00000 SCALE2 0.000000 0.030352 0.001268 0.00000 SCALE3 0.000000 0.000000 0.015727 0.00000 CONECT 2196 2197 2198 2199 CONECT 2197 2196 CONECT 2198 2196 CONECT 2199 2196 CONECT 2200 2201 2202 CONECT 2201 2200 CONECT 2202 2200 2203 2204 CONECT 2203 2202 CONECT 2204 2202 2205 CONECT 2205 2204 CONECT 2206 2207 2208 CONECT 2207 2206 CONECT 2208 2206 2209 2210 CONECT 2209 2208 CONECT 2210 2208 2211 CONECT 2211 2210 CONECT 2212 2226 2235 2237 2238 CONECT 2213 2227 2228 2239 2240 CONECT 2214 2228 2229 2241 CONECT 2215 2229 2230 2242 CONECT 2216 2217 2233 2234 CONECT 2217 2216 2218 2243 CONECT 2218 2217 2232 2244 CONECT 2219 2232 2233 2245 CONECT 2220 2221 2234 2236 CONECT 2221 2220 2222 2246 2247 CONECT 2222 2221 2248 2249 2250 CONECT 2223 2224 2226 2234 2251 CONECT 2224 2223 2225 2252 2253 CONECT 2225 2224 2235 2254 2255 CONECT 2226 2212 2223 2256 2257 CONECT 2227 2213 2235 2258 2259 CONECT 2228 2213 2214 2231 CONECT 2229 2214 2215 2260 CONECT 2230 2215 2231 2261 CONECT 2231 2228 2230 2262 CONECT 2232 2218 2219 2263 CONECT 2233 2216 2219 2264 CONECT 2234 2216 2220 2223 CONECT 2235 2212 2225 2227 CONECT 2236 2220 CONECT 2237 2212 CONECT 2238 2212 CONECT 2239 2213 CONECT 2240 2213 CONECT 2241 2214 CONECT 2242 2215 CONECT 2243 2217 CONECT 2244 2218 CONECT 2245 2219 CONECT 2246 2221 CONECT 2247 2221 CONECT 2248 2222 CONECT 2249 2222 CONECT 2250 2222 CONECT 2251 2223 CONECT 2252 2224 CONECT 2253 2224 CONECT 2254 2225 CONECT 2255 2225 CONECT 2256 2226 CONECT 2257 2226 CONECT 2258 2227 CONECT 2259 2227 CONECT 2260 2229 CONECT 2261 2230 CONECT 2262 2231 CONECT 2263 2232 CONECT 2264 2233 CONECT 2265 2266 2267 CONECT 2266 2265 CONECT 2267 2265 2268 2269 CONECT 2268 2267 CONECT 2269 2267 2270 CONECT 2270 2269 CONECT 2271 2272 2273 CONECT 2272 2271 CONECT 2273 2271 2274 2275 CONECT 2274 2273 CONECT 2275 2273 2276 CONECT 2276 2275 MASTER 216 0 6 4 20 0 0 6 2341 2 81 22 END