HEADER DE NOVO PROTEIN 19-DEC-23 8VEI TITLE DE NOVO DESIGNED COLIC ACID BINDER CHD_R1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHD_R1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO DESIGNED PROTEIN, SMALL MOLECULE BINDER, COLIC ACID, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,L.AN,D.BAKER REVDAT 2 31-JUL-24 8VEI 1 JRNL REVDAT 1 17-JUL-24 8VEI 0 JRNL AUTH L.AN,M.SAID,L.TRAN,S.MAJUMDER,I.GORESHNIK,G.R.LEE, JRNL AUTH 2 D.JUERGENS,J.DAUPARAS,I.ANISHCHENKO,B.COVENTRY,A.K.BERA, JRNL AUTH 3 A.KANG,P.M.LEVINE,V.ALVAREZ,A.PILLAI,C.NORN,D.FELDMAN, JRNL AUTH 4 D.ZORINE,D.R.HICKS,X.LI,M.G.SANCHEZ,D.K.VAFEADOS, JRNL AUTH 5 P.J.SALVESON,A.A.VOROBIEVA,D.BAKER JRNL TITL BINDING AND SENSING DIVERSE SMALL MOLECULES USING JRNL TITL 2 SHAPE-COMPLEMENTARY PSEUDOCYCLES. JRNL REF SCIENCE V. 385 276 2024 JRNL REFN ESSN 1095-9203 JRNL PMID 39024436 JRNL DOI 10.1126/SCIENCE.ADN3780 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 7662 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 766 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 42.5600 - 3.4700 1.00 1457 162 0.2126 0.2526 REMARK 3 2 3.4600 - 2.7500 1.00 1386 154 0.2297 0.2626 REMARK 3 3 2.7500 - 2.4000 1.00 1375 152 0.2276 0.2620 REMARK 3 4 2.4000 - 2.1800 1.00 1340 149 0.2570 0.2979 REMARK 3 5 2.1800 - 2.0300 0.98 1338 149 0.3061 0.3414 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) : 0.274 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.43 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 : 0.002 1020 REMARK 3 ANGLE : 0.432 1369 REMARK 3 CHIRALITY : 0.032 144 REMARK 3 PLANARITY : 0.002 167 REMARK 3 DIHEDRAL : 3.913 129 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): 11.6844 10.9232 -12.6666 REMARK 3 T TENSOR REMARK 3 T11: 0.3306 T22: 0.3057 REMARK 3 T33: 0.4740 T12: 0.0224 REMARK 3 T13: 0.0073 T23: -0.0859 REMARK 3 L TENSOR REMARK 3 L11: 4.2678 L22: 3.3345 REMARK 3 L33: 2.6928 L12: 0.7244 REMARK 3 L13: 0.6036 L23: 0.2001 REMARK 3 S TENSOR REMARK 3 S11: -0.1102 S12: -0.4303 S13: 0.4470 REMARK 3 S21: 0.1891 S22: 0.0009 S23: 0.2944 REMARK 3 S31: -0.0728 S32: -0.2336 S33: 0.1198 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 8VEI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7672 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 46.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.24700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 1.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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 (%): 36.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS/BIOCINE PH 8.5, 25% V/V 2 REMARK 280 -METHYL-2,4-PENTANEDIOL (MPD); 25% PEG1000; 25% W/V PEG 3350 AND REMARK 280 0.093 MSODIUM FLUORIDE; 0.3 M SODIUM BROMIDE; 0.3 M SODIUM REMARK 280 IODIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 42.56000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.56000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.12100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.90950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.12100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.90950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.56000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.12100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.90950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.56000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.12100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 28.90950 REMARK 290 SMTRY3 8 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 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 GLY A -1 REMARK 465 GLY A 0 REMARK 465 PRO A 1 REMARK 465 ILE A 2 REMARK 465 SER A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 122 REMARK 465 SER A 123 REMARK 465 GLY A 124 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 A 108 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 ARG A 80 -38.83 -130.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VEI A -1 124 PDB 8VEI 8VEI -1 124 SEQRES 1 A 126 GLY GLY PRO ILE GLU SER ALA LYS ILE PHE LYS GLU PHE SEQRES 2 A 126 LEU GLU ASP TYR GLU SER GLY LYS LYS SER PHE ARG GLU SEQRES 3 A 126 ALA SER TYR ASP ALA THR VAL LYS LEU PHE LEU TRP PHE SEQRES 4 A 126 LEU PRO ARG ASN ILE GLU LEU ALA GLU ILE ALA LEU ARG SEQRES 5 A 126 TRP LEU ILE MET LEU GLU SER LYS LYS VAL SER PHE GLU SEQRES 6 A 126 GLU ALA SER LEU ILE ALA LEU ARG GLU ALA LEU ARG TRP SEQRES 7 A 126 PHE LYS VAL ARG ASN ASN GLU LEU TYR LYS ILE ILE LYS SEQRES 8 A 126 GLU ALA LEU ASP ASP TYR GLU SER GLY LYS LYS SER PHE SEQRES 9 A 126 GLU GLU ALA LEU TRP ASP TYR TYR GLU LYS VAL LEU GLU SEQRES 10 A 126 TYR LEU LEU LYS SER GLY GLY SER GLY FORMUL 2 HOH *33(H2 O) HELIX 1 AA1 GLU A 3 SER A 17 1 15 HELIX 2 AA2 SER A 21 LEU A 38 1 18 HELIX 3 AA3 ASN A 41 SER A 57 1 17 HELIX 4 AA4 SER A 61 VAL A 79 1 19 HELIX 5 AA5 ASN A 81 SER A 97 1 17 HELIX 6 AA6 SER A 101 LYS A 119 1 19 CRYST1 46.242 57.819 85.120 90.00 90.00 90.00 C 2 2 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 0.021625 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011748 0.00000