HEADER LIPID BINDING PROTEIN 17-MAR-22 7UCZ TITLE THE CRYSTAL STRUCTURE OF APO MONOMER F57:H:H:H:H:H:H:R58 MUTANT OF TITLE 2 HCRBPII WITH HISTIDINE INSERTION IN THE HINGE LOOP REGION AT 1.1 TITLE 3 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 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 7UCZ 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. 1.08 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) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 101916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 27.0600 - 2.6000 0.97 7481 150 0.1857 0.1759 REMARK 3 2 2.6000 - 2.0600 0.97 7442 142 0.1976 0.2457 REMARK 3 3 2.0600 - 1.8000 0.96 7419 148 0.1941 0.2202 REMARK 3 4 1.8000 - 1.6400 0.96 7312 145 0.2002 0.2154 REMARK 3 5 1.6400 - 1.5200 0.95 7313 148 0.1896 0.1878 REMARK 3 6 1.5200 - 1.4300 0.94 7181 150 0.2046 0.2675 REMARK 3 7 1.4300 - 1.3600 0.94 7153 144 0.2124 0.2284 REMARK 3 8 1.3600 - 1.3000 0.93 7157 148 0.2165 0.2155 REMARK 3 9 1.3000 - 1.2500 0.92 7070 145 0.2264 0.2269 REMARK 3 10 1.2500 - 1.2100 0.92 7071 138 0.2260 0.2373 REMARK 3 11 1.2100 - 1.1700 0.91 6973 144 0.2264 0.2200 REMARK 3 12 1.1700 - 1.1400 0.90 6854 133 0.2334 0.2559 REMARK 3 13 1.1400 - 1.1100 0.90 6903 140 0.2418 0.2770 REMARK 3 14 1.1100 - 1.0800 0.85 6584 128 0.2556 0.2343 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) : 0.094 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.567 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.94 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 : 0.004 2385 REMARK 3 ANGLE : 0.744 3226 REMARK 3 CHIRALITY : 0.083 344 REMARK 3 PLANARITY : 0.004 417 REMARK 3 DIHEDRAL : 21.248 884 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): 1.8637 24.8288 6.8079 REMARK 3 T TENSOR REMARK 3 T11: 0.0779 T22: 0.0891 REMARK 3 T33: 0.1018 T12: -0.0029 REMARK 3 T13: -0.0023 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.1393 L22: 0.4031 REMARK 3 L33: 0.8182 L12: -0.0035 REMARK 3 L13: 0.0418 L23: 0.3673 REMARK 3 S TENSOR REMARK 3 S11: -0.0032 S12: 0.0105 S13: 0.0081 REMARK 3 S21: 0.0146 S22: 0.0032 S23: 0.0062 REMARK 3 S31: -0.0192 S32: 0.0188 S33: -0.0051 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 7UCZ 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_1000263949. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101925 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.079 REMARK 200 RESOLUTION RANGE LOW (A) : 27.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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 (%): 38.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, AMMONIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 LYS B 52 CG CD CE NZ REMARK 470 ARG B 64 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 66 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP B 119 CG OD1 OD2 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 83 -108.75 -121.91 REMARK 500 HIS B 63 -76.26 -102.07 REMARK 500 SER B 82 -12.39 83.75 REMARK 500 LEU B 83 -99.51 -116.52 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 339 DISTANCE = 6.76 ANGSTROMS DBREF 7UCZ A 1 139 UNP P50120 RET2_HUMAN 2 134 DBREF 7UCZ B 1 139 UNP P50120 RET2_HUMAN 2 134 SEQADV 7UCZ HIS A 58 UNP P50120 INSERTION SEQADV 7UCZ HIS A 59 UNP P50120 INSERTION SEQADV 7UCZ HIS A 60 UNP P50120 INSERTION SEQADV 7UCZ HIS A 61 UNP P50120 INSERTION SEQADV 7UCZ HIS A 62 UNP P50120 INSERTION SEQADV 7UCZ HIS A 63 UNP P50120 INSERTION SEQADV 7UCZ HIS B 58 UNP P50120 INSERTION SEQADV 7UCZ HIS B 59 UNP P50120 INSERTION SEQADV 7UCZ HIS B 60 UNP P50120 INSERTION SEQADV 7UCZ HIS B 61 UNP P50120 INSERTION SEQADV 7UCZ HIS B 62 UNP P50120 INSERTION SEQADV 7UCZ HIS B 63 UNP P50120 INSERTION SEQRES 1 A 139 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 A 139 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 139 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 A 139 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 A 139 THR THR SER THR PHE HIS HIS HIS HIS HIS HIS ARG ASN SEQRES 6 A 139 TYR ASP VAL ASP PHE THR VAL GLY VAL GLU PHE ASP GLU SEQRES 7 A 139 TYR THR LYS SER LEU ASP ASN ARG HIS VAL LYS ALA LEU SEQRES 8 A 139 VAL THR TRP GLU GLY ASP VAL LEU VAL CYS VAL GLN LYS SEQRES 9 A 139 GLY GLU LYS GLU ASN ARG GLY TRP LYS GLN TRP ILE GLU SEQRES 10 A 139 GLY ASP LYS LEU TYR LEU GLU LEU THR CYS GLY ASP GLN SEQRES 11 A 139 VAL CYS ARG GLN VAL PHE LYS LYS LYS SEQRES 1 B 139 THR ARG ASP GLN ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 B 139 GLU ASN PHE GLU GLY TYR MET LYS ALA LEU ASP ILE ASP SEQRES 3 B 139 PHE ALA THR ARG LYS ILE ALA VAL ARG LEU THR GLN THR SEQRES 4 B 139 LYS VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 B 139 THR THR SER THR PHE HIS HIS HIS HIS HIS HIS ARG ASN SEQRES 6 B 139 TYR ASP VAL ASP PHE THR VAL GLY VAL GLU PHE ASP GLU SEQRES 7 B 139 TYR THR LYS SER LEU ASP ASN ARG HIS VAL LYS ALA LEU SEQRES 8 B 139 VAL THR TRP GLU GLY ASP VAL LEU VAL CYS VAL GLN LYS SEQRES 9 B 139 GLY GLU LYS GLU ASN ARG GLY TRP LYS GLN TRP ILE GLU SEQRES 10 B 139 GLY ASP LYS LEU TYR LEU GLU LEU THR CYS GLY ASP GLN SEQRES 11 B 139 VAL CYS ARG GLN VAL PHE LYS LYS LYS FORMUL 3 HOH *264(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 ASP A 26 ALA A 33 1 8 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 ARG A 64 THR A 71 0 SHEET 2 AA110 ASN A 48 THR A 56 -1 N PHE A 49 O PHE A 70 SHEET 3 AA110 THR A 37 ASP A 45 -1 N ASP A 45 O ASN A 48 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N GLY A 6 O ILE A 42 SHEET 5 AA110 GLN A 130 LYS A 138 -1 O VAL A 135 N GLU A 11 SHEET 6 AA110 LYS A 120 CYS A 127 -1 N LEU A 125 O CYS A 132 SHEET 7 AA110 GLY A 111 GLU A 117 -1 N TRP A 115 O TYR A 122 SHEET 8 AA110 VAL A 98 LYS A 104 -1 N CYS A 101 O TRP A 112 SHEET 9 AA110 HIS A 87 GLU A 95 -1 N THR A 93 O VAL A 100 SHEET 10 AA110 PHE A 76 TYR A 79 -1 N PHE A 76 O ALA A 90 SHEET 1 AA210 HIS B 61 THR B 71 0 SHEET 2 AA210 ASN B 48 PHE B 57 -1 N PHE B 49 O PHE B 70 SHEET 3 AA210 THR B 37 ASP B 45 -1 N THR B 39 O THR B 54 SHEET 4 AA210 GLY B 6 GLU B 14 -1 N TRP B 8 O LYS B 40 SHEET 5 AA210 GLN B 130 LYS B 138 -1 O VAL B 135 N GLU B 11 SHEET 6 AA210 LYS B 120 CYS B 127 -1 N LEU B 123 O GLN B 134 SHEET 7 AA210 ARG B 110 GLU B 117 -1 N TRP B 115 O TYR B 122 SHEET 8 AA210 VAL B 98 LYS B 104 -1 N CYS B 101 O TRP B 112 SHEET 9 AA210 HIS B 87 GLU B 95 -1 N THR B 93 O VAL B 100 SHEET 10 AA210 PHE B 76 TYR B 79 -1 N PHE B 76 O ALA B 90 CRYST1 29.608 36.931 68.513 73.41 83.92 66.06 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 0.033775 -0.014996 0.000417 0.00000 SCALE2 0.000000 0.029626 -0.008201 0.00000 SCALE3 0.000000 0.000000 0.015230 0.00000