HEADER LIPID BINDING PROTEIN 12-APR-21 7MFY TITLE THE CRYSTAL STRUCTURE OF Q108K:K40L:T51V:T53S:R58W:Y19W:A33W:L117E TITLE 2 MUTANT OF HCRBPII BOUND WITH LIZFLUOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 2; COMPND 3 CHAIN: A; 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 DOMAIN SWAPPED TRIMER, ILBP, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GHANBARPOUR,J.GEIGER REVDAT 2 18-OCT-23 7MFY 1 REMARK REVDAT 1 12-JAN-22 7MFY 0 JRNL AUTH E.M.SANTOS,W.SHENG,R.ESMATPOUR SALMANI,S.TAHMASEBI NICK, JRNL AUTH 2 A.GHANBARPOUR,H.GHOLAMI,C.VASILEIOU,J.H.GEIGER,B.BORHAN JRNL TITL DESIGN OF LARGE STOKES SHIFT FLUORESCENT PROTEINS BASED ON JRNL TITL 2 EXCITED STATE PROTON TRANSFER OF AN ENGINEERED PHOTOBASE. JRNL REF J.AM.CHEM.SOC. V. 143 15091 2021 JRNL REFN ESSN 1520-5126 JRNL PMID 34516091 JRNL DOI 10.1021/JACS.1C05039 REMARK 2 REMARK 2 RESOLUTION. 1.26 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) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 32198 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.210 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 33.3000 - 3.0300 0.99 2182 142 0.1513 0.1513 REMARK 3 2 3.0300 - 2.4100 1.00 2183 145 0.1650 0.1843 REMARK 3 3 2.4100 - 2.1000 1.00 2194 146 0.1543 0.1644 REMARK 3 4 2.1000 - 1.9100 1.00 2167 144 0.1486 0.1853 REMARK 3 5 1.9100 - 1.7700 1.00 2191 148 0.1501 0.1786 REMARK 3 6 1.7700 - 1.6700 1.00 2171 141 0.1578 0.1804 REMARK 3 7 1.6700 - 1.5800 1.00 2177 146 0.1608 0.1771 REMARK 3 8 1.5800 - 1.5200 1.00 2157 140 0.1607 0.1966 REMARK 3 9 1.5200 - 1.4600 1.00 2172 142 0.1886 0.2194 REMARK 3 10 1.4600 - 1.4100 1.00 2184 144 0.1992 0.2504 REMARK 3 11 1.4100 - 1.3600 1.00 2162 144 0.2051 0.2259 REMARK 3 12 1.3600 - 1.3200 0.99 2147 147 0.2173 0.2554 REMARK 3 13 1.3200 - 1.2900 0.99 2166 138 0.2295 0.2697 REMARK 3 14 1.2900 - 1.2600 0.92 1947 131 0.2575 0.2634 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) : 0.103 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.53 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 : 0.006 1190 REMARK 3 ANGLE : 0.838 1606 REMARK 3 CHIRALITY : 0.089 167 REMARK 3 PLANARITY : 0.005 203 REMARK 3 DIHEDRAL : 9.183 700 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): 2.7914 17.7260 15.4446 REMARK 3 T TENSOR REMARK 3 T11: 0.1090 T22: 0.1047 REMARK 3 T33: 0.1116 T12: -0.0014 REMARK 3 T13: -0.0024 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.4712 L22: 0.4129 REMARK 3 L33: 0.9605 L12: -0.1012 REMARK 3 L13: 0.1040 L23: 0.0333 REMARK 3 S TENSOR REMARK 3 S11: -0.0025 S12: 0.0235 S13: -0.0080 REMARK 3 S21: -0.0824 S22: -0.0165 S23: 0.0108 REMARK 3 S31: -0.0384 S32: 0.0209 S33: 0.0000 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 7MFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000256007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-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-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 MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32216 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.258 REMARK 200 RESOLUTION RANGE LOW (A) : 33.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.44100 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: 2RCT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 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: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 14.45900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.30850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.45900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.30850 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 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 OD1 ASP A 24 O HOH A 301 2.04 REMARK 500 O HOH A 430 O HOH A 469 2.15 REMARK 500 O HOH A 323 O HOH A 363 2.18 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 PHE A 57 27.80 -141.61 REMARK 500 LYS A 75 -121.14 53.88 REMARK 500 LEU A 77 -77.25 -85.33 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 476 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 477 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 478 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 479 DISTANCE = 6.78 ANGSTROMS DBREF 7MFY A 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 7MFY TRP A 19 UNP P50120 TYR 20 ENGINEERED MUTATION SEQADV 7MFY TRP A 33 UNP P50120 ALA 34 ENGINEERED MUTATION SEQADV 7MFY LEU A 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 7MFY VAL A 51 UNP P50120 THR 52 ENGINEERED MUTATION SEQADV 7MFY SER A 53 UNP P50120 THR 54 ENGINEERED MUTATION SEQADV 7MFY TRP A 58 UNP P50120 ARG 59 ENGINEERED MUTATION SEQADV 7MFY LYS A 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQADV 7MFY GLU A 117 UNP P50120 LEU 118 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 TRP MET LYS ALA LEU ASP ILE ASP SEQRES 3 A 133 PHE ALA THR ARG LYS ILE TRP VAL ARG LEU THR GLN THR SEQRES 4 A 133 LEU VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS VAL LYS SEQRES 5 A 133 SER THR SER THR PHE TRP 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 GLU SEQRES 10 A 133 GLU LEU THR CYS GLY ASP GLN VAL CYS ARG GLN VAL PHE SEQRES 11 A 133 LYS LYS LYS HET ACT A 201 4 HET ZFG A 202 18 HET GOL A 203 6 HET GOL A 204 6 HET GOL A 205 6 HETNAM ACT ACETATE ION HETNAM ZFG 4-{5-[(2E)-BUT-2-EN-2-YL]THIOPHEN-2-YL}-N,N- HETNAM 2 ZFG DIMETHYLANILINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 ZFG C16 H19 N S FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *179(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 THR A 74 ASN A 79 1 6 SHEET 1 AA110 TRP A 58 THR A 65 0 SHEET 2 AA110 ASN A 48 SER A 55 -1 N SER A 53 O TYR A 60 SHEET 3 AA110 THR A 39 ASP A 45 -1 N ASP A 43 O LYS A 50 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O LEU A 40 SHEET 5 AA110 GLN A 124 LYS A 132 -1 O VAL A 129 N GLU A 11 SHEET 6 AA110 LYS A 114 CYS A 121 -1 N LEU A 119 O CYS A 126 SHEET 7 AA110 GLY A 105 GLU A 111 -1 N TRP A 109 O TYR A 116 SHEET 8 AA110 VAL A 92 LYS A 98 -1 N LEU A 93 O LYS A 108 SHEET 9 AA110 HIS A 81 GLU A 89 -1 N THR A 87 O VAL A 94 SHEET 10 AA110 PHE A 70 TYR A 73 -1 N PHE A 70 O ALA A 84 LINK NZ LYS A 108 C01 ZFG A 202 1555 1555 1.43 CRYST1 28.918 66.617 63.262 90.00 90.98 90.00 C 1 2 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 0.034581 0.000000 0.000592 0.00000 SCALE2 0.000000 0.015011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015810 0.00000