HEADER RETINOL-BINDING PROTEIN 07-MAR-23 8GEM TITLE CRYSTAL STRUCTURE OF HUMAN CELLULAR RETINOL BINDING PROTEIN 1 IN TITLE 2 COMPLEX WITH N-ETHYL-N-({3-[1-(4-METHYLPHENYL)CYCLOPENTYL]-1,2,4- TITLE 3 OXADIAZOL-5-YL}METHYL)-2-(1H-PYRAZOL-1-YL)ETHANAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 1; COMPND 3 CHAIN: B; 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: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE KEYWDS RBP1, CRBP1, RETINOL-BINDING, RETINOL, VITAMIN A, RETINOL-BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.PLAU,M.GOLCZAK REVDAT 2 01-NOV-23 8GEM 1 JRNL REVDAT 1 04-OCT-23 8GEM 0 JRNL AUTH J.PLAU,C.E.MORGAN,Y.FEDOROV,S.BANERJEE,D.J.ADAMS,W.S.BLANER, JRNL AUTH 2 E.W.YU,M.GOLCZAK JRNL TITL DISCOVERY OF NONRETINOID INHIBITORS OF CRBP1: STRUCTURAL AND JRNL TITL 2 DYNAMIC INSIGHTS FOR LIGAND-BINDING MECHANISMS. JRNL REF ACS CHEM.BIOL. V. 18 2309 2023 JRNL REFN ESSN 1554-8937 JRNL PMID 37713257 JRNL DOI 10.1021/ACSCHEMBIO.3C00402 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21274 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1119 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 46.8300 - 3.1000 0.99 2665 147 0.1729 0.2036 REMARK 3 2 3.1000 - 2.4600 1.00 2528 157 0.2245 0.2542 REMARK 3 3 2.4600 - 2.1500 1.00 2499 165 0.2366 0.2780 REMARK 3 4 2.1500 - 1.9500 1.00 2506 133 0.2609 0.3636 REMARK 3 5 1.9500 - 1.8100 1.00 2460 162 0.2767 0.3494 REMARK 3 6 1.8100 - 1.7100 1.00 2497 128 0.2908 0.3931 REMARK 3 7 1.7100 - 1.6200 1.00 2486 106 0.3002 0.4016 REMARK 3 8 1.6200 - 1.5500 1.00 2514 121 0.3397 0.4317 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.868 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.38 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 : 0.018 1177 REMARK 3 ANGLE : 1.505 1585 REMARK 3 CHIRALITY : 0.102 164 REMARK 3 PLANARITY : 0.010 202 REMARK 3 DIHEDRAL : 21.643 159 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 8GEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-20 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21341 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 46.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.88700 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 (%): 41.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5 AND 25% POLY REMARK 280 ETHYLENE GLYCOL 3350 (W/V)., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 18.86850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.83400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.02900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.83400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.86850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.02900 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: 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 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 MET B 0 REMARK 465 PRO B 1 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS B 139 REMARK 465 HIS B 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 HZ1 LYS B 131 O HOH B 301 1.55 REMARK 500 O HOH B 358 O HOH B 451 1.95 REMARK 500 O HOH B 375 O HOH B 445 2.11 REMARK 500 O HOH B 303 O HOH B 389 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 VAL B 2 CG1 - CB - CG2 ANGL. DEV. = 11.2 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 ILE B 77 -88.99 -100.73 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GEM B 0 134 UNP P09455 RET1_HUMAN 1 135 SEQADV 8GEM HIS B 135 UNP P09455 EXPRESSION TAG SEQADV 8GEM HIS B 136 UNP P09455 EXPRESSION TAG SEQADV 8GEM HIS B 137 UNP P09455 EXPRESSION TAG SEQADV 8GEM HIS B 138 UNP P09455 EXPRESSION TAG SEQADV 8GEM HIS B 139 UNP P09455 EXPRESSION TAG SEQADV 8GEM HIS B 140 UNP P09455 EXPRESSION TAG SEQRES 1 B 141 MET PRO VAL ASP PHE THR GLY TYR TRP LYS MET LEU VAL SEQRES 2 B 141 ASN GLU ASN PHE GLU GLU TYR LEU ARG ALA LEU ASP VAL SEQRES 3 B 141 ASN VAL ALA LEU ARG LYS ILE ALA ASN LEU LEU LYS PRO SEQRES 4 B 141 ASP LYS GLU ILE VAL GLN ASP GLY ASP HIS MET ILE ILE SEQRES 5 B 141 ARG THR LEU SER THR PHE ARG ASN TYR ILE MET ASP PHE SEQRES 6 B 141 GLN VAL GLY LYS GLU PHE GLU GLU ASP LEU THR GLY ILE SEQRES 7 B 141 ASP ASP ARG LYS CYS MET THR THR VAL SER TRP ASP GLY SEQRES 8 B 141 ASP LYS LEU GLN CYS VAL GLN LYS GLY GLU LYS GLU GLY SEQRES 9 B 141 ARG GLY TRP THR GLN TRP ILE GLU GLY ASP GLU LEU HIS SEQRES 10 B 141 LEU GLU MET ARG VAL GLU GLY VAL VAL CYS LYS GLN VAL SEQRES 11 B 141 PHE LYS LYS VAL GLN HIS HIS HIS HIS HIS HIS HET ZDF B 201 28 HETNAM ZDF N-ETHYL-N-({3-[1-(4-METHYLPHENYL)CYCLOPENTYL]-1,2,4- HETNAM 2 ZDF OXADIAZOL-5-YL}METHYL)-2-(1H-PYRAZOL-1-YL)ETHAN-1- HETNAM 3 ZDF AMINE FORMUL 2 ZDF C22 H29 N5 O FORMUL 3 HOH *158(H2 O) HELIX 1 AA1 ASN B 15 LEU B 23 1 9 HELIX 2 AA2 ASN B 26 LEU B 36 1 11 SHEET 1 AA110 TYR B 60 GLN B 65 0 SHEET 2 AA110 HIS B 48 LEU B 54 -1 N THR B 53 O TYR B 60 SHEET 3 AA110 ASP B 39 ASP B 45 -1 N GLU B 41 O ARG B 52 SHEET 4 AA110 GLY B 6 GLU B 14 -1 N TRP B 8 O LYS B 40 SHEET 5 AA110 VAL B 124 VAL B 133 -1 O LYS B 127 N GLU B 14 SHEET 6 AA110 GLU B 114 VAL B 121 -1 N LEU B 117 O GLN B 128 SHEET 7 AA110 GLY B 105 GLU B 111 -1 N TRP B 109 O HIS B 116 SHEET 8 AA110 LYS B 92 LYS B 98 -1 N CYS B 95 O TRP B 106 SHEET 9 AA110 LYS B 81 ASP B 89 -1 N ASP B 89 O LYS B 92 SHEET 10 AA110 PHE B 70 ASP B 73 -1 N GLU B 72 O CYS B 82 CRYST1 37.737 40.058 93.668 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 0.026499 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010676 0.00000