HEADER RETINOL-BINDING PROTEIN 06-MAR-23 8GDM TITLE CRYSTAL STRUCTURE OF HUMAN CELLULAR RETINOL BINDING PROTEIN 1 IN TITLE 2 COMPLEX WITH {[3-(DIPHENYLMETHYL)-1,2,4-OXADIAZOL-5- TITLE 3 YL]METHYL}(METHYL)[1-(THIOPHEN-2-YL)ETHYL]AMINE 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: 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 8GDM 1 JRNL REVDAT 1 04-OCT-23 8GDM 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 13005 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 1179 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 36.0400 - 3.6000 0.92 2629 196 0.1467 0.1695 REMARK 3 2 3.6000 - 2.8600 0.87 2549 136 0.1672 0.1811 REMARK 3 3 2.8600 - 2.5000 0.90 2670 122 0.2026 0.2512 REMARK 3 4 2.5000 - 2.2700 0.92 2664 137 0.1968 0.2850 REMARK 3 5 2.2700 - 2.1100 0.92 2681 158 0.2226 0.2675 REMARK 3 6 2.1100 - 1.9800 0.94 2746 150 0.2269 0.3459 REMARK 3 7 1.9800 - 1.8800 0.94 2784 117 0.2606 0.3191 REMARK 3 8 1.8800 - 1.8000 0.94 2718 163 0.2994 0.3576 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) : 0.255 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.20 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 1200 REMARK 3 ANGLE : 0.944 1618 REMARK 3 CHIRALITY : 0.051 168 REMARK 3 PLANARITY : 0.004 208 REMARK 3 DIHEDRAL : 10.977 156 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 8GDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-21 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13005 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 94.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.71300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 6E5L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 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 18.67450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.01350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.50750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.01350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.67450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.50750 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 MET A 0 REMARK 465 PRO A 1 REMARK 465 HIS A 138 REMARK 465 HIS A 139 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 411 O HOH A 427 1.98 REMARK 500 O HOH A 310 O HOH A 432 2.00 REMARK 500 OD1 ASP A 79 O HOH A 301 2.02 REMARK 500 O HOH A 312 O HOH A 395 2.10 REMARK 500 O HOH A 445 O HOH A 450 2.12 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 LYS A 31 CD - CE - NZ ANGL. DEV. = 16.4 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 A 77 -80.86 -108.60 REMARK 500 VAL A 121 125.48 -171.69 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 452 DISTANCE = 7.15 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8GD2 RELATED DB: PDB REMARK 900 8DG2 CONTAINS THE SAME PROTEIN WITH RELATED LIGAND DBREF 8GDM A 0 134 UNP P09455 RET1_HUMAN 1 135 SEQADV 8GDM HIS A 135 UNP P09455 EXPRESSION TAG SEQADV 8GDM HIS A 136 UNP P09455 EXPRESSION TAG SEQADV 8GDM HIS A 137 UNP P09455 EXPRESSION TAG SEQADV 8GDM HIS A 138 UNP P09455 EXPRESSION TAG SEQADV 8GDM HIS A 139 UNP P09455 EXPRESSION TAG SEQADV 8GDM HIS A 140 UNP P09455 EXPRESSION TAG SEQRES 1 A 141 MET PRO VAL ASP PHE THR GLY TYR TRP LYS MET LEU VAL SEQRES 2 A 141 ASN GLU ASN PHE GLU GLU TYR LEU ARG ALA LEU ASP VAL SEQRES 3 A 141 ASN VAL ALA LEU ARG LYS ILE ALA ASN LEU LEU LYS PRO SEQRES 4 A 141 ASP LYS GLU ILE VAL GLN ASP GLY ASP HIS MET ILE ILE SEQRES 5 A 141 ARG THR LEU SER THR PHE ARG ASN TYR ILE MET ASP PHE SEQRES 6 A 141 GLN VAL GLY LYS GLU PHE GLU GLU ASP LEU THR GLY ILE SEQRES 7 A 141 ASP ASP ARG LYS CYS MET THR THR VAL SER TRP ASP GLY SEQRES 8 A 141 ASP LYS LEU GLN CYS VAL GLN LYS GLY GLU LYS GLU GLY SEQRES 9 A 141 ARG GLY TRP THR GLN TRP ILE GLU GLY ASP GLU LEU HIS SEQRES 10 A 141 LEU GLU MET ARG VAL GLU GLY VAL VAL CYS LYS GLN VAL SEQRES 11 A 141 PHE LYS LYS VAL GLN HIS HIS HIS HIS HIS HIS HET ZA6 A 201 28 HETNAM ZA6 (1S)-N-{[3-(DIPHENYLMETHYL)-1,2,4-OXADIAZOL-5- HETNAM 2 ZA6 YL]METHYL}-N-METHYL-1-(THIOPHEN-2-YL)ETHAN-1-AMINE FORMUL 2 ZA6 C23 H23 N3 O S FORMUL 3 HOH *152(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASN A 26 LEU A 35 1 10 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 ASP A 45 O HIS A 48 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 LYS A 131 N LYS A 9 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 TRP A 109 O HIS A 116 SHEET 8 AA110 LYS A 92 LYS A 98 -1 N LEU A 93 O GLN A 108 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 GLU A 72 O CYS A 82 CRYST1 37.349 39.015 94.027 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 0.026774 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010635 0.00000