HEADER LIPID BINDING PROTEIN 20-APR-19 6ON7 TITLE CRYSTAL STRUCTURE OF APO DOMAIN-SWAPPED DIMER Q108K:T51D:A28C:L36C TITLE 2 MUTANT OF HUMAN CELLULAR RETINOL BINDING PROTEIN II 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: BACTERIAL EXPRESSION VECTOR PBEN1-SGC; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 747347 KEYWDS RETINOL, ILBP, PROTEIN SWITCH, CYTOSOLIC PROTEIN, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GHANBARPOUR,J.GEIGER REVDAT 4 11-OCT-23 6ON7 1 REMARK REVDAT 3 18-DEC-19 6ON7 1 REMARK REVDAT 2 13-NOV-19 6ON7 1 JRNL REVDAT 1 16-OCT-19 6ON7 0 JRNL AUTH A.GHANBARPOUR,C.PINGER,R.ESMATPOUR SALMANI,Z.ASSAR, JRNL AUTH 2 E.M.SANTOS,M.NOSRATI,K.PAWLOWSKI,D.SPENCE,C.VASILEIOU,X.JIN, JRNL AUTH 3 B.BORHAN,J.H.GEIGER JRNL TITL ENGINEERING THE HCRBPII DOMAIN-SWAPPED DIMER INTO A NEW JRNL TITL 2 CLASS OF PROTEIN SWITCHES. JRNL REF J.AM.CHEM.SOC. V. 141 17125 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 31557439 JRNL DOI 10.1021/JACS.9B04664 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 17684 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1751 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 31.4735 - 4.6540 0.91 1227 140 0.1772 0.1940 REMARK 3 2 4.6540 - 3.6959 0.81 1075 117 0.1717 0.2374 REMARK 3 3 3.6959 - 3.2292 0.93 1240 132 0.2099 0.2470 REMARK 3 4 3.2292 - 2.9342 0.96 1272 143 0.2212 0.2976 REMARK 3 5 2.9342 - 2.7240 0.96 1256 138 0.2335 0.2872 REMARK 3 6 2.7240 - 2.5635 0.97 1296 139 0.2299 0.2940 REMARK 3 7 2.5635 - 2.4352 0.98 1275 141 0.2225 0.2772 REMARK 3 8 2.4352 - 2.3292 0.84 1105 123 0.2045 0.2298 REMARK 3 9 2.3292 - 2.2396 0.93 1218 145 0.2031 0.2839 REMARK 3 10 2.2396 - 2.1623 0.96 1260 129 0.2032 0.2820 REMARK 3 11 2.1623 - 2.0947 0.96 1260 151 0.2091 0.2764 REMARK 3 12 2.0947 - 2.0348 0.96 1249 130 0.2058 0.2693 REMARK 3 13 2.0348 - 1.9813 0.90 1200 123 0.2187 0.2743 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.330 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 : 0.008 2222 REMARK 3 ANGLE : 0.951 2993 REMARK 3 CHIRALITY : 0.054 323 REMARK 3 PLANARITY : 0.004 386 REMARK 3 DIHEDRAL : 3.217 1867 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 6ON7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000239255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97624 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.981 REMARK 200 RESOLUTION RANGE LOW (A) : 31.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.810 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: 2RCT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, AMMONIUM ACETATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.09850 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 TYR A 60 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 58 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 60 CG CD1 CD2 CE1 CE2 CZ OH 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 TYR A 60 128.51 -175.30 REMARK 500 THR A 74 29.10 -70.15 REMARK 500 LYS A 75 137.59 -33.56 REMARK 500 SER A 76 -51.34 98.10 REMARK 500 LEU A 77 -95.09 -101.08 REMARK 500 ARG B 2 30.77 -82.11 REMARK 500 ASP B 24 24.24 86.38 REMARK 500 ASP B 26 138.66 -38.10 REMARK 500 ASN B 59 -153.24 80.32 REMARK 500 THR B 74 46.75 -77.79 REMARK 500 SER B 76 -37.96 113.77 REMARK 500 LEU B 77 -102.74 -126.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 6ON7 A 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 6ON7 B 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 6ON7 CYS A 28 UNP P50120 ALA 29 ENGINEERED MUTATION SEQADV 6ON7 CYS A 36 UNP P50120 LEU 37 ENGINEERED MUTATION SEQADV 6ON7 ASP A 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 6ON7 LYS A 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQADV 6ON7 CYS B 28 UNP P50120 ALA 29 ENGINEERED MUTATION SEQADV 6ON7 CYS B 36 UNP P50120 LEU 37 ENGINEERED MUTATION SEQADV 6ON7 ASP B 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 6ON7 LYS B 108 UNP P50120 GLN 109 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 CYS THR ARG LYS ILE ALA VAL ARG CYS THR GLN THR SEQRES 4 A 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS ASP 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 LYS 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 CYS THR ARG LYS ILE ALA VAL ARG CYS THR GLN THR SEQRES 4 B 133 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS ASP 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 LYS 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 FORMUL 3 HOH *35(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASP A 26 VAL A 34 1 9 HELIX 3 AA3 ASN B 15 LEU B 23 1 9 HELIX 4 AA4 ASP B 26 VAL B 34 1 9 SHEET 1 AA111 PHE A 70 TYR A 73 0 SHEET 2 AA111 HIS A 81 GLU A 89 -1 O ALA A 84 N PHE A 70 SHEET 3 AA111 VAL A 92 LYS A 98 -1 O VAL A 94 N THR A 87 SHEET 4 AA111 GLY A 105 GLU A 111 -1 O TRP A 106 N CYS A 95 SHEET 5 AA111 LYS A 114 CYS A 121 -1 O TYR A 116 N TRP A 109 SHEET 6 AA111 GLN A 124 LYS A 132 -1 O CYS A 126 N LEU A 119 SHEET 7 AA111 GLY B 6 GLU B 14 -1 O GLU B 11 N VAL A 129 SHEET 8 AA111 THR B 37 ASP B 45 -1 O LYS B 40 N TRP B 8 SHEET 9 AA111 ASN B 48 PHE B 57 -1 O LYS B 50 N ASP B 43 SHEET 10 AA111 ASN A 48 THR A 65 -1 N PHE A 64 O PHE B 49 SHEET 11 AA111 ASP B 61 THR B 65 -1 O PHE B 64 N PHE A 49 SHEET 1 AA218 PHE A 70 TYR A 73 0 SHEET 2 AA218 HIS A 81 GLU A 89 -1 O ALA A 84 N PHE A 70 SHEET 3 AA218 VAL A 92 LYS A 98 -1 O VAL A 94 N THR A 87 SHEET 4 AA218 GLY A 105 GLU A 111 -1 O TRP A 106 N CYS A 95 SHEET 5 AA218 LYS A 114 CYS A 121 -1 O TYR A 116 N TRP A 109 SHEET 6 AA218 GLN A 124 LYS A 132 -1 O CYS A 126 N LEU A 119 SHEET 7 AA218 GLY B 6 GLU B 14 -1 O GLU B 11 N VAL A 129 SHEET 8 AA218 THR B 37 ASP B 45 -1 O LYS B 40 N TRP B 8 SHEET 9 AA218 ASN B 48 PHE B 57 -1 O LYS B 50 N ASP B 43 SHEET 10 AA218 ASN A 48 THR A 65 -1 N PHE A 64 O PHE B 49 SHEET 11 AA218 THR A 37 ASP A 45 -1 N THR A 37 O THR A 56 SHEET 12 AA218 GLY A 6 GLU A 14 -1 N TRP A 8 O LYS A 40 SHEET 13 AA218 GLN B 124 LYS B 132 -1 O VAL B 129 N GLU A 11 SHEET 14 AA218 LYS B 114 CYS B 121 -1 N LEU B 117 O GLN B 128 SHEET 15 AA218 GLY B 105 GLU B 111 -1 N TRP B 109 O TYR B 116 SHEET 16 AA218 VAL B 92 LYS B 98 -1 N CYS B 95 O TRP B 106 SHEET 17 AA218 HIS B 81 GLU B 89 -1 N GLU B 89 O VAL B 92 SHEET 18 AA218 PHE B 70 TYR B 73 -1 N PHE B 70 O ALA B 84 SSBOND 1 CYS A 28 CYS B 28 1555 1555 2.07 CRYST1 36.506 60.197 63.071 90.00 93.70 90.00 P 1 21 1 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 0.027393 0.000000 0.001774 0.00000 SCALE2 0.000000 0.016612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015888 0.00000