HEADER RETINOL BINDING PROTEIN 28-AUG-24 9DDU TITLE Q108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L MUTANT OF HCRBPII BOUND TITLE 2 TO FR1V AND IRRADIATED WITH UV LIGHT AT PH 3.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL-BINDING PROTEIN 2; COMPND 3 CHAIN: B, A; 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN CELLULAR RETINOL BINDING PROTEIN II, HCRBPII, PROTEIN KEYWDS 2 ENGINEERING, FLUORESCENT PROTEIN, FR1V, RETINOL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.BINGHAM,J.H.GEIGER REVDAT 1 12-FEB-25 9DDU 0 JRNL AUTH C.BINGHAM,N.EHYEAI,S.MAITY,J.CANTRELL,J.GWASDACUS,W.SHENG, JRNL AUTH 2 C.VASILEIOU,B.BORHAN,J.H.GEIGER JRNL TITL PHOTOSWITCHING FLUORESCENCE VIA A NOVEL TRP-FLAP MECHANISM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 29102 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.96 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 : 0.017 2337 REMARK 3 ANGLE : 1.151 3147 REMARK 3 CHIRALITY : 0.075 329 REMARK 3 PLANARITY : 0.009 391 REMARK 3 DIHEDRAL : 19.714 1346 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 9DDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 - 4.8 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) : 1.272 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 : 29102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.599 REMARK 200 RESOLUTION RANGE LOW (A) : 29.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 88.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, AMMONIUM ACETATE, SODIUM REMARK 280 ACETATE, PH 4.0-4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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: 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 350 REMARK 350 BIOMOLECULE: 2 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 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 ASP B 61 CG OD1 OD2 REMARK 470 LYS A 52 CG CD CE NZ 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 OE2 GLU A 72 OXT ACY A 205 1.69 REMARK 500 O2 GOL A 206 O HOH A 301 1.84 REMARK 500 OD1 ASP A 47 O HOH A 302 1.93 REMARK 500 N THR A 1 OD1 ASP A 91 2.03 REMARK 500 O HOH A 339 O HOH A 352 2.12 REMARK 500 OG SER B 12 O HOH B 301 2.12 REMARK 500 OE2 GLU B 72 O ACY B 202 2.18 REMARK 500 O HOH B 340 O HOH B 349 2.19 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 B 57 -70.78 -97.20 REMARK 500 LEU B 77 -104.41 -119.41 REMARK 500 LEU A 77 -109.13 -124.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 102 -11.36 REMARK 500 GLU A 102 -11.36 REMARK 500 ASN A 103 -11.16 REMARK 500 ASN A 103 -11.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 9DDU B 1 133 UNP P50120 RET2_HUMAN 2 134 DBREF 9DDU A 1 133 UNP P50120 RET2_HUMAN 2 134 SEQADV 9DDU ALA B 4 UNP P50120 GLN 5 ENGINEERED MUTATION SEQADV 9DDU TRP B 19 UNP P50120 TYR 20 ENGINEERED MUTATION SEQADV 9DDU LEU B 29 UNP P50120 THR 30 ENGINEERED MUTATION SEQADV 9DDU LEU B 38 UNP P50120 GLN 39 ENGINEERED MUTATION SEQADV 9DDU LEU B 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 9DDU CYS B 53 UNP P50120 THR 54 ENGINEERED MUTATION SEQADV 9DDU TYR B 58 UNP P50120 ARG 59 ENGINEERED MUTATION SEQADV 9DDU LYS B 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQADV 9DDU ALA A 4 UNP P50120 GLN 5 ENGINEERED MUTATION SEQADV 9DDU TRP A 19 UNP P50120 TYR 20 ENGINEERED MUTATION SEQADV 9DDU LEU A 29 UNP P50120 THR 30 ENGINEERED MUTATION SEQADV 9DDU LEU A 38 UNP P50120 GLN 39 ENGINEERED MUTATION SEQADV 9DDU LEU A 40 UNP P50120 LYS 41 ENGINEERED MUTATION SEQADV 9DDU CYS A 53 UNP P50120 THR 54 ENGINEERED MUTATION SEQADV 9DDU TYR A 58 UNP P50120 ARG 59 ENGINEERED MUTATION SEQADV 9DDU LYS A 108 UNP P50120 GLN 109 ENGINEERED MUTATION SEQRES 1 B 133 THR ARG ASP ALA ASN GLY THR TRP GLU MET GLU SER ASN SEQRES 2 B 133 GLU ASN PHE GLU GLY TRP MET LYS ALA LEU ASP ILE ASP SEQRES 3 B 133 PHE ALA LEU ARG LYS ILE ALA VAL ARG LEU THR LEU THR SEQRES 4 B 133 LEU VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 B 133 CYS THR SER THR PHE TYR 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 SEQRES 1 A 133 THR ARG ASP ALA 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 LEU ARG LYS ILE ALA VAL ARG LEU THR LEU THR SEQRES 4 A 133 LEU VAL ILE ASP GLN ASP GLY ASP ASN PHE LYS THR LYS SEQRES 5 A 133 CYS THR SER THR PHE TYR 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 HET ZFJ B 201 48 HET ACY B 202 4 HET GOL B 203 6 HET GOL B 204 6 HET GOL B 205 6 HET GOL B 206 6 HET GOL B 207 6 HET ZFJ A 201 48 HET GOL A 202 6 HET GOL A 203 6 HET ACY A 204 4 HET ACY A 205 4 HET GOL A 206 6 HETNAM ZFJ (4AP)-N,N-DIETHYL-9,9-DIMETHYL-7-[(1E)-PROP-1-EN-1-YL]- HETNAM 2 ZFJ 9H-FLUOREN-2-AMINE HETNAM ACY ACETIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZFJ 2(C22 H27 N) FORMUL 4 ACY 3(C2 H4 O2) FORMUL 5 GOL 8(C3 H8 O3) FORMUL 16 HOH *110(H2 O) HELIX 1 AA1 ASN B 15 LEU B 23 1 9 HELIX 2 AA2 ASP B 26 VAL B 34 1 9 HELIX 3 AA3 ASN A 15 LEU A 23 1 9 HELIX 4 AA4 ASP A 26 VAL A 34 1 9 SHEET 1 AA110 ASN B 59 THR B 65 0 SHEET 2 AA110 ASN B 48 THR B 54 -1 N THR B 51 O VAL B 62 SHEET 3 AA110 THR B 39 ASP B 45 -1 N VAL B 41 O LYS B 52 SHEET 4 AA110 GLY B 6 GLU B 14 -1 N TRP B 8 O LEU B 40 SHEET 5 AA110 GLN B 124 LYS B 132 -1 O VAL B 129 N GLU B 11 SHEET 6 AA110 LYS B 114 CYS B 121 -1 N LEU B 117 O GLN B 128 SHEET 7 AA110 GLY B 105 GLU B 111 -1 N TRP B 109 O TYR B 116 SHEET 8 AA110 VAL B 92 LYS B 98 -1 N CYS B 95 O TRP B 106 SHEET 9 AA110 HIS B 81 GLU B 89 -1 N THR B 87 O VAL B 94 SHEET 10 AA110 PHE B 70 TYR B 73 -1 N GLU B 72 O VAL B 82 SHEET 1 AA210 ASN A 59 THR A 65 0 SHEET 2 AA210 ASN A 48 THR A 54 -1 N THR A 51 O VAL A 62 SHEET 3 AA210 THR A 39 ASP A 45 -1 N THR A 39 O THR A 54 SHEET 4 AA210 GLY A 6 GLU A 14 -1 N TRP A 8 O LEU A 40 SHEET 5 AA210 GLN A 124 LYS A 132 -1 O VAL A 129 N GLU A 11 SHEET 6 AA210 LYS A 114 CYS A 121 -1 N LEU A 117 O GLN A 128 SHEET 7 AA210 GLY A 105 GLU A 111 -1 N TRP A 109 O TYR A 116 SHEET 8 AA210 VAL A 92 LYS A 98 -1 N CYS A 95 O TRP A 106 SHEET 9 AA210 HIS A 81 GLU A 89 -1 N THR A 87 O VAL A 94 SHEET 10 AA210 PHE A 70 TYR A 73 -1 N PHE A 70 O ALA A 84 LINK NZ LYS B 108 C23 ZFJ B 201 1555 1555 1.42 LINK NZ LYS A 108 C23 ZFJ A 201 1555 1555 1.29 CRYST1 31.021 35.939 64.043 86.01 86.51 65.28 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 0.032236 -0.014841 -0.001245 0.00000 SCALE2 0.000000 0.030632 -0.001493 0.00000 SCALE3 0.000000 0.000000 0.015662 0.00000