HEADER DE NOVO PROTEIN 23-MAY-23 8P4Y TITLE COILED-COIL PROTEIN ORIGAMI TRIANGLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ORIGAMI TRIANGLE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RESIDUE 171 HAS POST-TRANSLATIONAL MODIFICATION. 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: NICO21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET-41A(+) KEYWDS COILED-COIL, PROTEIN ORIGAMI, DESIGNED PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.SATLER,S.HADZI,R.JERALA REVDAT 3 23-AUG-23 8P4Y 1 JRNL REVDAT 2 16-AUG-23 8P4Y 1 SOURCE REVDAT 1 02-AUG-23 8P4Y 0 JRNL AUTH T.SATLER,S.HADZI,R.JERALA JRNL TITL CRYSTAL STRUCTURE OF DE NOVO DESIGNED COILED-COIL PROTEIN JRNL TITL 2 ORIGAMI TRIANGLE. JRNL REF J.AM.CHEM.SOC. V. 145 16995 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37486611 JRNL DOI 10.1021/JACS.3C05531 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 12490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 625 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 36.3470 - 3.2563 0.97 2966 157 0.1771 0.2241 REMARK 3 2 3.2563 - 2.5849 0.98 2997 158 0.2659 0.3099 REMARK 3 3 2.5849 - 2.2582 0.98 2957 155 0.2407 0.3095 REMARK 3 4 2.2582 - 2.0520 0.97 2945 155 0.2922 0.3558 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.00 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 1657 REMARK 3 ANGLE : 0.747 2194 REMARK 3 CHIRALITY : 0.041 227 REMARK 3 PLANARITY : 0.004 290 REMARK 3 DIHEDRAL : 18.131 1073 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2871 -6.6309 45.8952 REMARK 3 T TENSOR REMARK 3 T11: 0.5698 T22: 0.5884 REMARK 3 T33: 0.6879 T12: -0.0106 REMARK 3 T13: 0.0048 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 4.5021 L22: 6.8273 REMARK 3 L33: 5.9728 L12: 0.7989 REMARK 3 L13: 1.7030 L23: 0.4375 REMARK 3 S TENSOR REMARK 3 S11: 0.3188 S12: 1.0826 S13: -0.2511 REMARK 3 S21: -0.7282 S22: -0.4040 S23: 0.1124 REMARK 3 S31: 0.5759 S32: 2.1771 S33: 0.1653 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 34 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9437 -22.8504 26.9579 REMARK 3 T TENSOR REMARK 3 T11: 0.6162 T22: 0.6494 REMARK 3 T33: 0.5481 T12: 0.0280 REMARK 3 T13: -0.0725 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 4.1327 L22: 5.4727 REMARK 3 L33: 4.9098 L12: -0.0439 REMARK 3 L13: -2.0083 L23: 2.8084 REMARK 3 S TENSOR REMARK 3 S11: 0.1862 S12: 0.2344 S13: -0.4544 REMARK 3 S21: -0.9979 S22: -0.5560 S23: 0.9750 REMARK 3 S31: 0.0183 S32: -0.4061 S33: 0.2206 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 66 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3070 -16.9075 52.1005 REMARK 3 T TENSOR REMARK 3 T11: 0.5031 T22: 0.6444 REMARK 3 T33: 0.7006 T12: -0.0120 REMARK 3 T13: 0.0734 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.9998 L22: 5.5183 REMARK 3 L33: 9.4457 L12: 1.9336 REMARK 3 L13: 3.3280 L23: 5.7909 REMARK 3 S TENSOR REMARK 3 S11: -0.0801 S12: -0.0799 S13: 0.2565 REMARK 3 S21: 0.0902 S22: -0.2573 S23: 1.2692 REMARK 3 S31: 0.0773 S32: -0.6445 S33: 0.4482 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.5065 0.4740 50.0226 REMARK 3 T TENSOR REMARK 3 T11: 0.6980 T22: 0.6559 REMARK 3 T33: 0.5516 T12: -0.0197 REMARK 3 T13: -0.0245 T23: 0.0854 REMARK 3 L TENSOR REMARK 3 L11: 5.2370 L22: 5.3645 REMARK 3 L33: 9.1655 L12: 0.4402 REMARK 3 L13: 6.8832 L23: 1.2934 REMARK 3 S TENSOR REMARK 3 S11: -0.8302 S12: 0.1253 S13: 1.1841 REMARK 3 S21: -0.1789 S22: 0.1031 S23: 0.5255 REMARK 3 S31: -0.7213 S32: 0.5878 S33: 0.7993 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 133 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1366 -18.2475 35.2688 REMARK 3 T TENSOR REMARK 3 T11: 0.7387 T22: 0.5464 REMARK 3 T33: 0.6955 T12: -0.0477 REMARK 3 T13: -0.0253 T23: -0.1142 REMARK 3 L TENSOR REMARK 3 L11: 2.0412 L22: 6.5934 REMARK 3 L33: 4.6116 L12: -2.0335 REMARK 3 L13: -1.1392 L23: -0.9600 REMARK 3 S TENSOR REMARK 3 S11: -0.2470 S12: -0.9488 S13: 0.0384 REMARK 3 S21: -0.0649 S22: 0.1778 S23: 1.0666 REMARK 3 S31: -0.0751 S32: -0.4703 S33: 0.1124 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 161 THROUGH 198 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6288 -20.0042 49.7658 REMARK 3 T TENSOR REMARK 3 T11: 0.5162 T22: 0.5370 REMARK 3 T33: 0.5403 T12: 0.0264 REMARK 3 T13: 0.0328 T23: 0.0508 REMARK 3 L TENSOR REMARK 3 L11: 3.1910 L22: 7.7925 REMARK 3 L33: 5.5082 L12: -0.2085 REMARK 3 L13: 2.1410 L23: 2.8726 REMARK 3 S TENSOR REMARK 3 S11: 0.3622 S12: 0.2515 S13: -0.2389 REMARK 3 S21: 0.8379 S22: 0.7114 S23: -1.1080 REMARK 3 S31: 0.9130 S32: 0.7081 S33: -0.9187 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 8P4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 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 : 12496 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 36.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.620 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.75 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.320 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 (%): 43.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PEG 400, 100 MM REMARK 280 CHES/SODIUMHYDROXIDE PH 9.5, 200 MM SODIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SER A 35 REMARK 465 GLY A 36 REMARK 465 GLY A 134 REMARK 465 GLY A 164 REMARK 465 SER A 165 REMARK 465 GLY A 199 REMARK 465 SER A 200 REMARK 465 GLY A 201 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 2 OG REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 ARG A 12 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 16 CG CD CE NZ REMARK 470 ARG A 19 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 33 CG CD OE1 OE2 REMARK 470 SER A 135 OG DBREF 8P4Y A 1 201 PDB 8P4Y 8P4Y 1 201 SEQRES 1 A 201 GLY SER PRO GLU ASP GLU ILE GLU ARG LEU GLU ARG GLU SEQRES 2 A 201 ASN GLU LYS LEU GLU ARG GLU ASN GLU ARG LEU GLU ARG SEQRES 3 A 201 GLU ILE ARG TRP LEU GLU GLU GLY SER GLY GLN LEU GLU SEQRES 4 A 201 ASP LYS VAL GLU GLU LEU LEU SER LYS ASN TYR HIS LEU SEQRES 5 A 201 GLU ASN GLU VAL GLU ARG LEU LYS LYS LEU VAL GLY SER SEQRES 6 A 201 GLY SER PRO GLU ASP LYS ILE GLU GLU LEU LYS ARG LYS SEQRES 7 A 201 ILE GLU LYS LEU LYS ARG GLU ASN GLU ARG LEU GLU ARG SEQRES 8 A 201 GLU ASN GLU TRP LEU GLU ARG GLY SER GLY SER PRO GLU SEQRES 9 A 201 ASP LYS ILE GLU GLU LEU LYS ARG LYS ASN ARG GLU LEU SEQRES 10 A 201 LYS GLU LYS ASN LYS GLU LEU LYS GLU LYS ILE TYR ARG SEQRES 11 A 201 LEU LYS GLU GLY SER GLY GLN LEU GLU ASP LYS VAL GLU SEQRES 12 A 201 GLU LEU LEU SER LYS ASN TYR HIS LEU GLU ASN GLU VAL SEQRES 13 A 201 GLU ARG LEU LYS LYS LEU VAL GLY SER GLY SER PRO GLU SEQRES 14 A 201 MEN GLU ILE LYS GLU LEU GLU GLU GLU ILE ARG GLU LEU SEQRES 15 A 201 GLU GLU LYS ASN GLU GLU LEU LYS ARG LYS ASN GLU TRP SEQRES 16 A 201 LEU LYS ARG GLY SER GLY HET MEN A 170 9 HET GOL A 301 6 HET GOL A 302 6 HET GOL A 303 6 HETNAM MEN N-METHYL ASPARAGINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MEN C5 H10 N2 O3 FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *18(H2 O) HELIX 1 AA1 SER A 2 GLY A 34 1 33 HELIX 2 AA2 LEU A 38 LEU A 62 1 25 HELIX 3 AA3 SER A 65 GLY A 99 1 35 HELIX 4 AA4 SER A 100 GLU A 133 1 34 HELIX 5 AA5 GLN A 137 LYS A 161 1 25 HELIX 6 AA6 SER A 167 ARG A 198 1 32 LINK C GLU A 169 N MEN A 170 1555 1555 1.32 LINK C MEN A 170 N GLU A 171 1555 1555 1.33 CRYST1 33.840 36.980 44.670 97.25 105.76 95.45 P 1 1 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 0.029551 0.002819 0.008900 0.00000 SCALE2 0.000000 0.027164 0.004365 0.00000 SCALE3 0.000000 0.000000 0.023559 0.00000