HEADER LIPID BINDING PROTEIN 17-MAR-22 7UCV TITLE THE CRYSTAL STRUCTURE OF APO DOMAIN-SWAPPED DIMER Q108K:T51D:A28CL36C TITLE 2 R58:H:H:H:N59 HCRBPII WITH HISTIDINE INSERTION IN THE HINGE LOOP TITLE 3 REGION AT 2.19 ANGSTROM RESOLUTION 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 LBP, CRBPII, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GHANBARPOUR,J.GEIGER REVDAT 1 18-OCT-23 7UCV 0 JRNL AUTH A.GHANBARPOUR,J.GEIGER JRNL TITL THE CRYSTAL STRUCTURE OF DOMAIN-SAWPPED DIMER JRNL TITL 2 Q108K:T51D:A28C:L36C:F57:H:R58 MUTANT OF HCRBPII WITH A JRNL TITL 3 HISTIDINE INSERTION IN THE HINGE LOOP REGION AT 1.96 JRNL TITL 4 ANGSTROM RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.19 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 14150 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1414 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 34.9500 - 4.7200 0.99 1437 159 0.1813 0.2024 REMARK 3 2 4.7200 - 3.7400 0.87 1198 133 0.1640 0.2243 REMARK 3 3 3.7400 - 3.2700 0.93 1253 139 0.1843 0.2788 REMARK 3 4 3.2700 - 2.9700 0.95 1280 142 0.2188 0.2836 REMARK 3 5 2.9700 - 2.7600 0.97 1306 145 0.2230 0.3337 REMARK 3 6 2.7600 - 2.6000 0.98 1284 143 0.2201 0.2815 REMARK 3 7 2.6000 - 2.4700 0.99 1284 142 0.2211 0.3176 REMARK 3 8 2.4700 - 2.3600 0.98 1311 147 0.2140 0.2767 REMARK 3 9 2.3600 - 2.2700 0.95 1238 137 0.2135 0.2919 REMARK 3 10 2.2700 - 2.1900 0.87 1145 127 0.2272 0.3251 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) : 0.293 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.036 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.78 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 : 0.007 2308 REMARK 3 ANGLE : 0.872 3107 REMARK 3 CHIRALITY : 0.056 326 REMARK 3 PLANARITY : 0.005 401 REMARK 3 DIHEDRAL : 17.638 1372 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): 27.8843 26.6364 12.9456 REMARK 3 T TENSOR REMARK 3 T11: 0.2016 T22: 0.1878 REMARK 3 T33: 0.1928 T12: -0.0040 REMARK 3 T13: 0.0034 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 0.6712 L22: 0.2451 REMARK 3 L33: 0.0965 L12: 0.3999 REMARK 3 L13: -0.1955 L23: -0.0918 REMARK 3 S TENSOR REMARK 3 S11: -0.0489 S12: 0.0572 S13: -0.0072 REMARK 3 S21: -0.0786 S22: 0.0305 S23: -0.0222 REMARK 3 S31: 0.0255 S32: -0.0050 S33: 0.0147 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 1 THROUGH 54 OR REMARK 3 RESID 56 THROUGH 60 OR RESID 62 THROUGH REMARK 3 136)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 1 THROUGH 54 OR REMARK 3 RESID 56 THROUGH 60 OR RESID 62 THROUGH REMARK 3 136)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7UCV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-18 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) : 0.97625 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 : 14150 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 34.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26400 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: 2RCQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, AMMONIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 18.47600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.62700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.95050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.62700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.47600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.95050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 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 LEU A 80 -96.77 -136.62 REMARK 500 LEU B 80 -100.72 -131.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UCV A 1 136 UNP P50120 RET2_HUMAN 2 134 DBREF 7UCV B 1 136 UNP P50120 RET2_HUMAN 2 134 SEQADV 7UCV CYS A 28 UNP P50120 ALA 29 ENGINEERED MUTATION SEQADV 7UCV CYS A 36 UNP P50120 LEU 37 ENGINEERED MUTATION SEQADV 7UCV ASP A 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 7UCV HIS A 59 UNP P50120 INSERTION SEQADV 7UCV HIS A 60 UNP P50120 INSERTION SEQADV 7UCV HIS A 61 UNP P50120 INSERTION SEQADV 7UCV LYS A 111 UNP P50120 GLN 109 ENGINEERED MUTATION SEQADV 7UCV CYS B 28 UNP P50120 ALA 29 ENGINEERED MUTATION SEQADV 7UCV CYS B 36 UNP P50120 LEU 37 ENGINEERED MUTATION SEQADV 7UCV ASP B 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 7UCV HIS B 59 UNP P50120 INSERTION SEQADV 7UCV HIS B 60 UNP P50120 INSERTION SEQADV 7UCV HIS B 61 UNP P50120 INSERTION SEQADV 7UCV LYS B 111 UNP P50120 GLN 109 ENGINEERED MUTATION SEQRES 1 A 136 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 A 136 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 136 PHE CYS THR ARG LYS ILE ALA VAL ARG CYS THR GLN THR SEQRES 4 A 136 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS ASP LYS SEQRES 5 A 136 THR THR SER THR PHE ARG HIS HIS HIS ASN TYR ASP VAL SEQRES 6 A 136 ASP PHE THR VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SEQRES 7 A 136 SER LEU ASP ASN ARG HIS VAL LYS ALA LEU VAL THR TRP SEQRES 8 A 136 GLU GLY ASP VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS SEQRES 9 A 136 GLU ASN ARG GLY TRP LYS LYS TRP ILE GLU GLY ASP LYS SEQRES 10 A 136 LEU TYR LEU GLU LEU THR CYS GLY ASP GLN VAL CYS ARG SEQRES 11 A 136 GLN VAL PHE LYS LYS LYS SEQRES 1 B 136 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 B 136 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 B 136 PHE CYS THR ARG LYS ILE ALA VAL ARG CYS THR GLN THR SEQRES 4 B 136 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS ASP LYS SEQRES 5 B 136 THR THR SER THR PHE ARG HIS HIS HIS ASN TYR ASP VAL SEQRES 6 B 136 ASP PHE THR VAL GLY VAL GLU PHE ASP GLU TYR THR LYS SEQRES 7 B 136 SER LEU ASP ASN ARG HIS VAL LYS ALA LEU VAL THR TRP SEQRES 8 B 136 GLU GLY ASP VAL LEU VAL CYS VAL GLN LYS GLY GLU LYS SEQRES 9 B 136 GLU ASN ARG GLY TRP LYS LYS TRP ILE GLU GLY ASP LYS SEQRES 10 B 136 LEU TYR LEU GLU LEU THR CYS GLY ASP GLN VAL CYS ARG SEQRES 11 B 136 GLN VAL PHE LYS LYS LYS FORMUL 3 HOH *48(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASP A 26 ARG A 35 1 10 HELIX 3 AA3 ASN B 15 LEU B 23 1 9 HELIX 4 AA4 ASP B 26 VAL B 34 1 9 SHEET 1 AA118 PHE A 73 TYR A 76 0 SHEET 2 AA118 HIS A 84 GLU A 92 -1 O ALA A 87 N PHE A 73 SHEET 3 AA118 VAL A 95 LYS A 101 -1 O VAL A 97 N THR A 90 SHEET 4 AA118 GLY A 108 GLU A 114 -1 O TRP A 109 N CYS A 98 SHEET 5 AA118 LYS A 117 CYS A 124 -1 O TYR A 119 N TRP A 112 SHEET 6 AA118 GLN A 127 LYS A 135 -1 O CYS A 129 N LEU A 122 SHEET 7 AA118 GLY B 6 GLU B 14 -1 O GLU B 9 N LYS A 134 SHEET 8 AA118 THR B 37 ASP B 45 -1 O LYS B 40 N TRP B 8 SHEET 9 AA118 ASN B 48 THR B 68 -1 O THR B 54 N THR B 39 SHEET 10 AA118 ASN A 48 THR A 68 -1 N PHE A 57 O HIS B 59 SHEET 11 AA118 THR A 37 ASP A 45 -1 N THR A 39 O THR A 54 SHEET 12 AA118 GLY A 6 GLU A 14 -1 N TRP A 8 O LYS A 40 SHEET 13 AA118 GLN B 127 LYS B 135 -1 O VAL B 132 N GLU A 11 SHEET 14 AA118 LYS B 117 CYS B 124 -1 N LEU B 120 O GLN B 131 SHEET 15 AA118 GLY B 108 GLU B 114 -1 N TRP B 112 O TYR B 119 SHEET 16 AA118 VAL B 95 LYS B 101 -1 N CYS B 98 O TRP B 109 SHEET 17 AA118 HIS B 84 GLU B 92 -1 N THR B 90 O VAL B 97 SHEET 18 AA118 PHE B 73 TYR B 76 -1 N PHE B 73 O ALA B 87 SSBOND 1 CYS A 28 CYS B 28 1555 1555 2.04 CRYST1 36.952 69.901 107.254 90.00 90.00 90.00 P 21 21 21 8 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 0.027062 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014306 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009324 0.00000