HEADER DE NOVO PROTEIN 21-MAY-25 9V3A TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED SEROTONIN BINDER SROB2_26_L7F COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRYSTAL STRUCTURE OF DE NOVO DESIGNED SEROTONIN BINDER COMPND 3 SROB2_26_L7F; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SMALL MOLECULE BINDING COMPLEX, DE NOVO PROTEIN, SEROTONIN BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,J.LIU,L.CAO REVDAT 1 27-MAY-26 9V3A 0 JRNL AUTH Y.ZHANG,L.CAO JRNL TITL DE NOVO DESIGN OF LIGAND BINDER AND SENSOR USIGN A JRNL TITL 2 PHYSICALLY GENERATIVE APPROACH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7301 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.190 REMARK 3 FREE R VALUE TEST SET COUNT : 774 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 26.9300 - 3.6300 1.00 1170 135 0.1790 0.2144 REMARK 3 2 3.6300 - 2.8800 1.00 1141 127 0.1793 0.2311 REMARK 3 3 2.8800 - 2.5200 0.99 1138 118 0.1922 0.2528 REMARK 3 4 2.5200 - 2.2900 0.99 1134 128 0.1958 0.3038 REMARK 3 5 2.2900 - 2.1300 0.99 1120 132 0.1773 0.2516 REMARK 3 6 2.1300 - 2.0000 0.97 1115 134 0.1925 0.2879 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.91 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 : 0.007 953 REMARK 3 ANGLE : 0.887 1278 REMARK 3 CHIRALITY : 0.045 143 REMARK 3 PLANARITY : 0.006 162 REMARK 3 DIHEDRAL : 16.942 369 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 9V3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 23-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059162. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 181 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7301 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12380 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.830 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 (%): 40.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25.5% (W/V) PEG 4000, 170 MM AMMONIUM REMARK 280 SULFATE, 15% (V/V) GLYCEROL, BATCH MODE, TEMPERATURE 291K 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 32.94650 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 78 REMARK 465 ASN A 79 REMARK 465 GLY A 80 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 GLU A 20 CG CD OE1 OE2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 GLU A 36 CG CD OE1 OE2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 LYS A 40 CG CD CE NZ REMARK 470 GLU A 47 CG CD OE1 OE2 DBREF 9V3A A -2 120 PDB 9V3A 9V3A -2 120 SEQRES 1 A 123 GLY PRO GLY ASP ALA ALA ARG LYS VAL PHE GLU TYR ALA SEQRES 2 A 123 GLU GLU LEU GLU LYS GLU GLY VAL PRO GLU GLU GLU ILE SEQRES 3 A 123 GLN LYS LYS PHE VAL GLU LEU ALA GLU LYS LEU LEU GLU SEQRES 4 A 123 GLU GLU SER LYS GLU THR GLY VAL PRO LEU GLU GLU VAL SEQRES 5 A 123 ARG LYS LYS PHE VAL ALA GLU LEU ILE ALA LEU THR ILE SEQRES 6 A 123 GLU LYS TYR GLY LEU GLU TYR ALA VAL LYS ILE ALA ASP SEQRES 7 A 123 LYS ILE LYS ASN GLY SER LYS HIS PRO LEU LEU GLN GLU SEQRES 8 A 123 PHE ALA GLU LYS VAL TYR GLU ILE GLU LYS GLU VAL LYS SEQRES 9 A 123 GLY LYS GLU ASN PRO GLU LYS LEU ALA LEU GLU LEU ALA SEQRES 10 A 123 LYS LYS LEU ALA GLU ALA HET SRO A 201 13 HET GOL A 202 6 HET GOL A 203 6 HETNAM SRO SEROTONIN HETNAM GOL GLYCEROL HETSYN SRO 3-(2-AMINOETHYL)-1H-INDOL-5-OL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SRO C10 H12 N2 O FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *194(H2 O) HELIX 1 AA1 GLY A -2 GLY A 17 1 20 HELIX 2 AA2 PRO A 19 GLY A 43 1 25 HELIX 3 AA3 PRO A 45 GLY A 66 1 22 HELIX 4 AA4 GLY A 66 LYS A 76 1 11 HELIX 5 AA5 HIS A 83 LYS A 101 1 19 HELIX 6 AA6 ASN A 105 ALA A 120 1 16 CRYST1 29.501 65.893 29.513 90.00 90.70 90.00 P 1 21 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 0.033897 0.000000 0.000413 0.00000 SCALE2 0.000000 0.015176 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033885 0.00000 CONECT 940 941 CONECT 941 940 942 949 CONECT 942 941 943 CONECT 943 942 944 CONECT 944 943 945 948 CONECT 945 944 946 CONECT 946 945 947 CONECT 947 946 948 950 CONECT 948 944 947 949 CONECT 949 941 948 CONECT 950 947 951 CONECT 951 950 952 CONECT 952 951 CONECT 953 954 955 CONECT 954 953 CONECT 955 953 956 957 CONECT 956 955 CONECT 957 955 958 CONECT 958 957 CONECT 959 960 961 CONECT 960 959 CONECT 961 959 962 963 CONECT 962 961 CONECT 963 961 964 CONECT 964 963 MASTER 211 0 3 6 0 0 0 6 1157 1 25 10 END