HEADER DE NOVO PROTEIN 27-APR-25 9R1K TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED ARCYRIAFLAVIN A BINDER, TITLE 2 SC-APCC-4-A7F-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC-4-A7F-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 9R1K 0 JRNL AUTH R.PETRENAS,K.OZGA,J.J.CHUBB,D.N.WOOLFSON JRNL TITL X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED ARCYRIAFLAVIN JRNL TITL 2 A BINDER, SC-APCC-4-A7F-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 298 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 27.9100 - 2.7700 1.00 2866 143 0.2122 0.2417 REMARK 3 2 2.7700 - 2.2000 1.00 2806 155 0.2362 0.2924 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) : 0.326 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.528 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.15 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 : 0.005 897 REMARK 3 ANGLE : 0.621 1222 REMARK 3 CHIRALITY : 0.038 149 REMARK 3 PLANARITY : 0.003 152 REMARK 3 DIHEDRAL : 18.545 294 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID -1 THROUGH 130) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6795 1.4780 13.2232 REMARK 3 T TENSOR REMARK 3 T11: 0.3204 T22: 0.3576 REMARK 3 T33: 0.2334 T12: -0.0600 REMARK 3 T13: -0.0001 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 2.7910 L22: 7.0838 REMARK 3 L33: 6.4299 L12: -2.1551 REMARK 3 L13: 1.6178 L23: -3.5555 REMARK 3 S TENSOR REMARK 3 S11: -0.0427 S12: -0.3262 S13: -0.2624 REMARK 3 S21: 0.4641 S22: 0.3677 S23: 0.0901 REMARK 3 S31: -0.0180 S32: -0.4036 S33: -0.3303 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 9R1K 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_1292147387. 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 : 7 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 : 5977 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 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 (%): 29.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH REMARK 280 7.0, 20 % W/V PEG 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 18.93000 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: 270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6650 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 465 GLN A 64 REMARK 465 GLY A 65 REMARK 465 GLY A 98 REMARK 465 GLY A 99 REMARK 465 THR A 100 REMARK 465 SER A 101 REMARK 465 GLN A 131 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 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 MET A 1 CG SD CE REMARK 470 GLN A 2 CG CD OE1 NE2 REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 GLU A 11 CD OE1 OE2 REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 LYS A 15 CG CD CE NZ REMARK 470 GLN A 16 CD OE1 NE2 REMARK 470 LYS A 18 NZ REMARK 470 LYS A 19 CG CD CE NZ REMARK 470 LYS A 26 CD CE NZ REMARK 470 GLN A 43 CD OE1 NE2 REMARK 470 GLU A 46 CD OE1 OE2 REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 61 CD CE NZ REMARK 470 SER A 68 OG REMARK 470 GLN A 70 CG CD OE1 NE2 REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 GLN A 76 CG CD OE1 NE2 REMARK 470 GLU A 80 CD OE1 OE2 REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 GLN A 84 CG CD OE1 NE2 REMARK 470 LYS A 86 CD CE NZ REMARK 470 LYS A 93 CE NZ REMARK 470 LYS A 94 CE NZ REMARK 470 GLU A 106 CG CD OE1 OE2 REMARK 470 GLU A 107 CD OE1 OE2 REMARK 470 GLN A 110 CG CD OE1 NE2 REMARK 470 GLU A 113 CD OE1 OE2 REMARK 470 GLU A 114 CD OE1 OE2 REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLN A 118 CG CD OE1 NE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 LYS A 127 CD CE NZ REMARK 470 LYS A 128 CG CD CE NZ DBREF 9R1K A -19 131 PDB 9R1K 9R1K -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 VAL 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 VAL SEQRES 6 A 151 GLU GLU ILE ALA LYS GLN LEU 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 SER LYS LYS ILE 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 GLY GLU GLU GLY ALA LYS GLN ALA LYS LYS ILE ALA SEQRES 12 A 151 TRP GLN LEU LYS LYS ILE ALA GLN HET EDO A 201 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 HOH *13(H2 O) HELIX 1 AA1 SER A -1 GLY A 30 1 32 HELIX 2 AA2 ALA A 34 ALA A 63 1 30 HELIX 3 AA3 ASP A 67 ALA A 96 1 30 HELIX 4 AA4 GLY A 103 ALA A 130 1 28 CRYST1 27.555 37.860 57.023 90.00 101.82 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 0.036291 0.000000 0.007595 0.00000 SCALE2 0.000000 0.026413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017917 0.00000 CONECT 883 884 885 CONECT 884 883 CONECT 885 883 886 CONECT 886 885 MASTER 280 0 1 4 0 0 0 6 876 1 4 12 END