HEADER DE NOVO PROTEIN 27-APR-25 9R1L TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED SN38 BINDER, SC-APCC-4- TITLE 2 SN38-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC-4-SN38-1; 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, COILED-COIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.PETRENAS,K.OZGA,J.J.CHUBB,D.N.WOOLFSON REVDAT 1 06-MAY-26 9R1L 0 JRNL AUTH R.PETRENAS,K.OZGA,J.J.CHUBB,D.N.WOOLFSON JRNL TITL X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED SN38 BINDER, JRNL TITL 2 SC-APCC-4-SN38-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 9615 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 437 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 27.2400 - 2.6600 1.00 3132 144 0.1903 0.2008 REMARK 3 2 2.6600 - 2.1100 1.00 3044 156 0.2272 0.2443 REMARK 3 3 2.1100 - 1.8500 0.99 3005 137 0.2637 0.2941 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) : 0.218 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.507 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.69 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 1009 REMARK 3 ANGLE : 0.568 1356 REMARK 3 CHIRALITY : 0.030 150 REMARK 3 PLANARITY : 0.002 180 REMARK 3 DIHEDRAL : 20.403 373 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.5859 -3.9284 12.2508 REMARK 3 T TENSOR REMARK 3 T11: 0.2727 T22: 0.3568 REMARK 3 T33: 0.3904 T12: -0.0499 REMARK 3 T13: 0.0354 T23: 0.1137 REMARK 3 L TENSOR REMARK 3 L11: 3.7784 L22: 7.0205 REMARK 3 L33: 6.9844 L12: -5.1501 REMARK 3 L13: 5.1478 L23: -7.0069 REMARK 3 S TENSOR REMARK 3 S11: -0.0825 S12: -0.5607 S13: -0.2719 REMARK 3 S21: -0.2912 S22: 0.4858 S23: 0.2140 REMARK 3 S31: 0.5969 S32: -0.8633 S33: -0.4718 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2162 -3.4360 7.5634 REMARK 3 T TENSOR REMARK 3 T11: 0.3384 T22: 0.2541 REMARK 3 T33: 0.3263 T12: 0.0019 REMARK 3 T13: -0.0038 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 1.7640 L22: 8.5060 REMARK 3 L33: 4.7738 L12: -3.8643 REMARK 3 L13: 2.8893 L23: -6.3618 REMARK 3 S TENSOR REMARK 3 S11: 0.1785 S12: -0.0264 S13: -0.1025 REMARK 3 S21: -0.5121 S22: -0.1202 S23: -0.2835 REMARK 3 S31: 0.5190 S32: 0.0422 S33: -0.1537 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4835 1.4465 16.5476 REMARK 3 T TENSOR REMARK 3 T11: 0.2256 T22: 0.1739 REMARK 3 T33: 0.1726 T12: -0.0377 REMARK 3 T13: 0.0169 T23: -0.0267 REMARK 3 L TENSOR REMARK 3 L11: 3.9470 L22: 8.3737 REMARK 3 L33: 6.3770 L12: -3.5220 REMARK 3 L13: 2.1089 L23: -3.7564 REMARK 3 S TENSOR REMARK 3 S11: -0.1534 S12: -0.0556 S13: 0.0226 REMARK 3 S21: 0.5550 S22: 0.1992 S23: -0.2459 REMARK 3 S31: -0.5464 S32: -0.3083 S33: -0.0247 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 9R1L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-25. REMARK 100 THE DEPOSITION ID IS D_1292147388. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9615 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 27.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG BUFFER PH 6.0, 25 % W/V PEG REMARK 280 1500, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 18.79050 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: 830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 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 SER A -1 OG REMARK 470 MET A 1 CG SD CE REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 GLN A 8 CD OE1 NE2 REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 LYS A 15 CE NZ REMARK 470 GLN A 16 CD OE1 NE2 REMARK 470 LYS A 26 CD CE NZ REMARK 470 GLN A 43 CG CD OE1 NE2 REMARK 470 LYS A 83 CE NZ REMARK 470 LYS A 86 CD CE NZ REMARK 470 LYS A 87 CD CE NZ REMARK 470 LYS A 94 CE NZ REMARK 470 GLN A 97 CG CD OE1 NE2 REMARK 470 SER A 101 OG REMARK 470 GLU A 106 CG CD OE1 OE2 REMARK 470 GLN A 110 CG CD OE1 NE2 REMARK 470 LYS A 117 CD CE NZ REMARK 470 LYS A 121 CD CE NZ REMARK 470 LYS A 127 CE NZ REMARK 470 LYS A 128 CG CD CE NZ DBREF 9R1L A -19 131 PDB 9R1L 9R1L -19 131 SEQRES 1 A 151 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 151 LEU VAL PRO ARG GLY SER HIS MET GLN LEU GLU GLU ILE SEQRES 3 A 151 ALA GLN GLN LEU GLU GLU GLY ALA LYS GLN THR LYS LYS SEQRES 4 A 151 ASN ALA TRP GLN LEU LYS LYS ILE ALA GLN GLY GLU PRO SEQRES 5 A 151 SER ALA GLN GLY GLN LEU GLU GLU ILE ALA GLN GLN ALA SEQRES 6 A 151 GLU GLU ILE ALA LYS GLN SER LYS LYS ILE ALA TRP GLN SEQRES 7 A 151 LEU LYS LYS ILE ALA GLN GLY PRO ASP SER VAL GLN LEU SEQRES 8 A 151 GLU GLU ILE ALA GLN GLN LEU GLU GLU ILE ALA LYS GLN SEQRES 9 A 151 ALA LYS LYS GLY ALA TRP GLN LEU LYS LYS ILE ALA GLN SEQRES 10 A 151 GLY GLY THR SER GLY GLY GLN LEU GLU GLU ILE ALA GLN SEQRES 11 A 151 GLN ALA GLU GLU GLY ALA LYS GLN ALA LYS LYS ILE ALA SEQRES 12 A 151 TRP GLN LEU LYS LYS ILE ALA GLN HET PEG A 301 17 HET ETA A 302 6 HET ETA A 303 6 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ETA ETHANOLAMINE FORMUL 2 PEG C4 H10 O3 FORMUL 3 ETA 2(C2 H7 N O) FORMUL 5 HOH *24(H2 O) HELIX 1 AA1 SER A -1 GLY A 30 1 32 HELIX 2 AA2 ALA A 34 GLY A 65 1 32 HELIX 3 AA3 ASP A 67 GLY A 99 1 33 HELIX 4 AA4 SER A 101 GLN A 131 1 31 CRYST1 27.763 37.581 54.860 90.00 101.16 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 0.036019 0.000000 0.007106 0.00000 SCALE2 0.000000 0.026609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018580 0.00000 CONECT 1935 1936 1937 1942 1943 CONECT 1936 1935 1944 CONECT 1937 1935 1938 1945 1946 CONECT 1938 1937 1939 CONECT 1939 1938 1940 1947 1948 CONECT 1940 1939 1941 1949 1950 CONECT 1941 1940 1951 CONECT 1942 1935 CONECT 1943 1935 CONECT 1944 1936 CONECT 1945 1937 CONECT 1946 1937 CONECT 1947 1939 CONECT 1948 1939 CONECT 1949 1940 CONECT 1950 1940 CONECT 1951 1941 CONECT 1952 1953 1954 1956 1957 CONECT 1953 1952 CONECT 1954 1952 1955 CONECT 1955 1954 CONECT 1956 1952 CONECT 1957 1952 CONECT 1958 1959 1960 1962 1963 CONECT 1959 1958 CONECT 1960 1958 1961 CONECT 1961 1960 CONECT 1962 1958 CONECT 1963 1958 MASTER 283 0 3 4 0 0 0 6 1012 1 29 12 END