HEADER DE NOVO PROTEIN 27-APR-25 9R1J TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED NILE RED BINDER, SC- TITLE 2 APCC-4-NR-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC-4-NR-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-COILS, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.PETRENAS,K.OZGA,J.J.CHUBB,D.N.WOOLFSON REVDAT 1 06-MAY-26 9R1J 0 JRNL AUTH R.PETRENAS,K.OZGA,J.J.CHUBB,D.N.WOOLFSON JRNL TITL X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED NILE RED JRNL TITL 2 BINDER, SC-APCC-4-NR-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 12142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 611 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 31.4700 - 2.7000 1.00 3121 161 0.1850 0.2102 REMARK 3 2 2.7000 - 2.1400 1.00 3035 162 0.1895 0.1742 REMARK 3 3 2.1400 - 1.8700 0.98 2975 172 0.1910 0.1956 REMARK 3 4 1.8700 - 1.7020 0.78 2388 116 0.1984 0.2300 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) : 0.146 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.936 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.03 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 : 0.006 989 REMARK 3 ANGLE : 0.522 1332 REMARK 3 CHIRALITY : 0.033 153 REMARK 3 PLANARITY : 0.002 171 REMARK 3 DIHEDRAL : 18.147 369 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0413 -3.8001 15.6959 REMARK 3 T TENSOR REMARK 3 T11: 0.1258 T22: 0.2124 REMARK 3 T33: 0.1304 T12: 0.0517 REMARK 3 T13: 0.0317 T23: -0.0464 REMARK 3 L TENSOR REMARK 3 L11: 1.6740 L22: 2.9447 REMARK 3 L33: 2.1811 L12: 0.9370 REMARK 3 L13: 0.9411 L23: 1.9165 REMARK 3 S TENSOR REMARK 3 S11: 0.0306 S12: 0.3717 S13: -0.2860 REMARK 3 S21: 0.1402 S22: 0.3897 S23: -0.3885 REMARK 3 S31: 0.3296 S32: 0.5194 S33: -0.1529 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 34 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0176 -4.1334 19.0388 REMARK 3 T TENSOR REMARK 3 T11: 0.1424 T22: 0.1339 REMARK 3 T33: 0.1173 T12: 0.0326 REMARK 3 T13: 0.0054 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.5875 L22: 3.3798 REMARK 3 L33: 2.0575 L12: 1.4331 REMARK 3 L13: 1.0953 L23: 1.6989 REMARK 3 S TENSOR REMARK 3 S11: 0.1169 S12: 0.1389 S13: -0.1078 REMARK 3 S21: 0.2944 S22: -0.0152 S23: 0.0948 REMARK 3 S31: 0.3492 S32: 0.0951 S33: -0.0857 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4268 2.1802 12.9243 REMARK 3 T TENSOR REMARK 3 T11: 0.1547 T22: 0.1660 REMARK 3 T33: 0.1352 T12: 0.0348 REMARK 3 T13: 0.0010 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 2.5751 L22: 5.6396 REMARK 3 L33: 2.4546 L12: 2.6329 REMARK 3 L13: 1.6850 L23: 2.3666 REMARK 3 S TENSOR REMARK 3 S11: -0.0488 S12: 0.1378 S13: 0.3444 REMARK 3 S21: 0.0416 S22: -0.1171 S23: 0.6070 REMARK 3 S31: 0.0141 S32: 0.0415 S33: 0.0778 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 102 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7727 2.6577 8.3779 REMARK 3 T TENSOR REMARK 3 T11: 0.2772 T22: 0.2282 REMARK 3 T33: 0.1500 T12: -0.0116 REMARK 3 T13: 0.0082 T23: 0.0274 REMARK 3 L TENSOR REMARK 3 L11: 3.8882 L22: 3.9496 REMARK 3 L33: 3.9787 L12: 2.8502 REMARK 3 L13: 2.7797 L23: 2.5783 REMARK 3 S TENSOR REMARK 3 S11: -0.2822 S12: 0.4134 S13: 0.2690 REMARK 3 S21: -0.2625 S22: 0.2167 S23: 0.1762 REMARK 3 S31: -0.1270 S32: 0.5851 S33: -0.0184 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 9R1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-25. REMARK 100 THE DEPOSITION ID IS D_1292147383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 : 12142 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.702 REMARK 200 RESOLUTION RANGE LOW (A) : 31.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.360 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 (%): 28.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MMT BUFFER PH 5.0, 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 19.08050 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: 310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7490 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 -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 SER A -7 REMARK 465 SER A -6 REMARK 465 GLY A -5 REMARK 465 GLU A -4 REMARK 465 ASN A -3 REMARK 465 LEU A -2 REMARK 465 TYR A -1 REMARK 465 PHE A 0 REMARK 465 GLN A 1 REMARK 465 SER 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 HIS A 3 CG ND1 CD2 CE1 NE2 REMARK 470 MET A 4 CG SD CE REMARK 470 GLU A 7 CD OE1 OE2 REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 GLN A 11 CG CD OE1 NE2 REMARK 470 GLU A 14 CD OE1 OE2 REMARK 470 GLU A 15 CG CD OE1 OE2 REMARK 470 GLN A 19 CD OE1 NE2 REMARK 470 LYS A 28 CE NZ REMARK 470 GLN A 46 CD OE1 NE2 REMARK 470 LYS A 56 CE NZ REMARK 470 LYS A 57 NZ REMARK 470 GLU A 83 CD OE1 OE2 REMARK 470 LYS A 86 CE NZ REMARK 470 LYS A 89 CE NZ REMARK 470 LYS A 90 CE NZ REMARK 470 LYS A 96 CE NZ REMARK 470 GLN A 100 CG CD OE1 NE2 REMARK 470 GLN A 107 CD OE1 NE2 REMARK 470 GLU A 109 CD OE1 OE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLN A 121 CD OE1 NE2 REMARK 470 LYS A 124 CE NZ REMARK 470 LYS A 131 CE NZ DBREF 9R1J A -17 134 PDB 9R1J 9R1J -17 134 SEQRES 1 A 152 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 152 GLU ASN LEU TYR PHE GLN SER HIS MET GLN LEU GLU GLU SEQRES 3 A 152 ILE ALA GLN GLN LEU GLU GLU GLY ALA LYS GLN ALA LYS SEQRES 4 A 152 LYS ALA ALA TRP GLN LEU LYS LYS ILE ALA GLN GLY GLU SEQRES 5 A 152 PRO SER ALA GLN GLY GLN LEU GLU GLU ILE ALA GLN GLN SEQRES 6 A 152 VAL GLU GLU ILE ALA LYS GLN ILE LYS LYS ILE ALA TRP SEQRES 7 A 152 GLN LEU LYS LYS ILE ALA GLN GLY PRO ASP SER VAL GLN SEQRES 8 A 152 LEU GLU GLU ILE ALA GLN GLN LEU GLU GLU ILE ALA LYS SEQRES 9 A 152 GLN VAL LYS LYS ILE ALA TRP GLN LEU LYS LYS ILE ALA SEQRES 10 A 152 GLN GLY GLY THR SER GLY GLY GLN LEU GLU GLU ILE ALA SEQRES 11 A 152 GLN GLN ALA GLU GLU GLY ALA LYS GLN ALA LYS LYS ILE SEQRES 12 A 152 ALA TRP GLN LEU LYS LYS ILE ALA GLN HET GOL A 201 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *125(H2 O) HELIX 1 AA1 HIS A 3 GLY A 33 1 31 HELIX 2 AA2 ALA A 37 ALA A 66 1 30 HELIX 3 AA3 ASP A 70 GLN A 100 1 31 HELIX 4 AA4 GLY A 106 GLN A 134 1 29 CRYST1 27.662 38.161 56.690 90.00 101.08 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 0.036151 0.000000 0.007079 0.00000 SCALE2 0.000000 0.026205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017975 0.00000 CONECT 1939 1940 1941 1945 1946 CONECT 1940 1939 1947 CONECT 1941 1939 1942 1943 1948 CONECT 1942 1941 1949 CONECT 1943 1941 1944 1950 1951 CONECT 1944 1943 1952 CONECT 1945 1939 CONECT 1946 1939 CONECT 1947 1940 CONECT 1948 1941 CONECT 1949 1942 CONECT 1950 1943 CONECT 1951 1943 CONECT 1952 1944 MASTER 304 0 1 4 0 0 0 6 1095 1 14 12 END