HEADER DE NOVO PROTEIN 08-JUN-25 9RGZ TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED SINGLE-CHAIN TITLE 2 ANTIPARALLEL 3-HELIX COILED-COIL BUNDLE, SC-APCC3-CW-2NTT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC3-CW-2NTT; COMPND 3 CHAIN: A, B; 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 COILED COIL, CC, DE NOVO, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.LENG,D.N.WOOLFSON REVDAT 3 22-OCT-25 9RGZ 1 JRNL REVDAT 2 01-OCT-25 9RGZ 1 JRNL REVDAT 1 03-SEP-25 9RGZ 0 JRNL AUTH X.LENG,K.I.ALBANESE,L.R.GOLUB,A.A.NORMAN,J.CLAYDEN, JRNL AUTH 2 D.N.WOOLFSON JRNL TITL DE NOVO DESIGNED 3-HELIX BUNDLE PEPTIDES AND PROTEINS WITH JRNL TITL 2 CONTROLLED TOPOLOGY AND STABILITY. JRNL REF CHEM SCI V. 16 18632 2025 JRNL REFN ISSN 2041-6520 JRNL PMID 40969159 JRNL DOI 10.1039/D5SC05576H REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 13707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 659 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 40.1200 - 3.5100 1.00 2687 137 0.1948 0.2100 REMARK 3 2 3.5000 - 2.7800 0.99 2626 110 0.2271 0.2307 REMARK 3 3 2.7800 - 2.4300 1.00 2597 136 0.2357 0.3139 REMARK 3 4 2.4300 - 2.2100 1.00 2549 153 0.2307 0.2871 REMARK 3 5 2.2100 - 2.0500 0.99 2589 123 0.2637 0.3596 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) : 0.227 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.868 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.60 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 : 0.003 1368 REMARK 3 ANGLE : 0.579 1870 REMARK 3 CHIRALITY : 0.026 243 REMARK 3 PLANARITY : 0.002 236 REMARK 3 DIHEDRAL : 15.248 472 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID -1 THROUGH 95) REMARK 3 ORIGIN FOR THE GROUP (A): 27.9076 0.3445 6.7321 REMARK 3 T TENSOR REMARK 3 T11: 0.5821 T22: 0.2681 REMARK 3 T33: 0.3442 T12: -0.0143 REMARK 3 T13: -0.0869 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 1.1602 L22: 0.4207 REMARK 3 L33: 4.9660 L12: -0.2913 REMARK 3 L13: 0.7111 L23: -0.0413 REMARK 3 S TENSOR REMARK 3 S11: 0.0891 S12: -0.0961 S13: 0.0049 REMARK 3 S21: -0.0002 S22: 0.2378 S23: -0.1943 REMARK 3 S31: 0.0264 S32: 0.2401 S33: -0.3117 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID -2 THROUGH 95) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7285 14.6477 5.5121 REMARK 3 T TENSOR REMARK 3 T11: 0.4697 T22: 0.2137 REMARK 3 T33: 0.2293 T12: 0.0190 REMARK 3 T13: -0.0399 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 0.9206 L22: 1.8311 REMARK 3 L33: 1.1224 L12: 0.0659 REMARK 3 L13: 0.0117 L23: 0.1883 REMARK 3 S TENSOR REMARK 3 S11: 0.0642 S12: 0.1195 S13: 0.0599 REMARK 3 S21: -0.1836 S22: -0.0435 S23: 0.0145 REMARK 3 S31: -0.1939 S32: 0.0530 S33: -0.0261 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 9RGZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1292148400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-24 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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13719 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 40.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06717 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5600 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) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45260 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.560 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 (%): 43.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE 0.1 M SODIUM HEPES, PH 7, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 24.22503 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.64300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.11539 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 24.22503 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.64300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 40.11539 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS 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 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 MET B -20 REMARK 465 GLY B -19 REMARK 465 SER B -18 REMARK 465 SER B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 LEU B -7 REMARK 465 VAL B -6 REMARK 465 PRO B -5 REMARK 465 ARG B -4 REMARK 465 GLY B -3 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 -1 CG ND1 CD2 CE1 NE2 REMARK 470 MET A 0 CG SD CE REMARK 470 MET A 1 CG SD CE REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 GLU A 7 CD OE1 OE2 REMARK 470 LYS A 8 CD CE NZ REMARK 470 LYS A 13 CD CE NZ REMARK 470 GLU A 14 CD OE1 OE2 REMARK 470 LYS A 15 NZ REMARK 470 LYS A 29 NZ REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 LYS A 48 CE NZ REMARK 470 GLU A 49 CD OE1 OE2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 ASN A 65 CG OD1 ND2 REMARK 470 LYS A 70 NZ REMARK 470 LYS A 77 CE NZ REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 SER B -2 OG REMARK 470 MET B 0 CG SD CE REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 GLU B 7 CG CD OE1 OE2 REMARK 470 LYS B 8 CD CE NZ REMARK 470 LYS B 13 CD CE NZ REMARK 470 GLU B 14 CD OE1 OE2 REMARK 470 LYS B 15 CE NZ REMARK 470 LYS B 22 CD CE NZ REMARK 470 GLU B 42 CD OE1 OE2 REMARK 470 LYS B 48 CD CE NZ REMARK 470 GLU B 49 CD OE1 OE2 REMARK 470 GLU B 56 CD OE1 OE2 REMARK 470 ASN B 65 CG OD1 ND2 REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 LYS B 77 CG CD CE NZ REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 LYS B 84 CG CD CE NZ REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 188 DISTANCE = 6.86 ANGSTROMS DBREF 9RGZ A -20 95 PDB 9RGZ 9RGZ -20 95 DBREF 9RGZ B -20 95 PDB 9RGZ 9RGZ -20 95 SEQRES 1 A 116 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 116 LEU VAL PRO ARG GLY SER HIS MET MET LEU ALA ALA LEU SEQRES 3 A 116 LYS GLU LYS ASN ALA ALA LEU LYS GLU LYS ASN ALA ALA SEQRES 4 A 116 LEU LYS TYR LYS LEU ALA ALA LEU LYS GLU LYS LEU GLY SEQRES 5 A 116 LEU THR PRO GLU LEU ALA ALA LEU GLU LYS GLU LEU ALA SEQRES 6 A 116 ALA THR GLU LYS GLU LEU ALA ALA THR GLU TRP GLU LEU SEQRES 7 A 116 ALA ALA LEU GLU ALA ASP PRO ASN PRO ASP PRO ALA LYS SEQRES 8 A 116 LEU ALA ALA LEU GLU LYS LYS THR ALA ALA LEU GLU LYS SEQRES 9 A 116 LYS THR ALA ALA LEU GLU TYR LYS LEU ALA ALA LEU SEQRES 1 B 116 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 116 LEU VAL PRO ARG GLY SER HIS MET MET LEU ALA ALA LEU SEQRES 3 B 116 LYS GLU LYS ASN ALA ALA LEU LYS GLU LYS ASN ALA ALA SEQRES 4 B 116 LEU LYS TYR LYS LEU ALA ALA LEU LYS GLU LYS LEU GLY SEQRES 5 B 116 LEU THR PRO GLU LEU ALA ALA LEU GLU LYS GLU LEU ALA SEQRES 6 B 116 ALA THR GLU LYS GLU LEU ALA ALA THR GLU TRP GLU LEU SEQRES 7 B 116 ALA ALA LEU GLU ALA ASP PRO ASN PRO ASP PRO ALA LYS SEQRES 8 B 116 LEU ALA ALA LEU GLU LYS LYS THR ALA ALA LEU GLU LYS SEQRES 9 B 116 LYS THR ALA ALA LEU GLU TYR LYS LEU ALA ALA LEU FORMUL 3 HOH *142(H2 O) HELIX 1 AA1 HIS A -1 GLY A 31 1 33 HELIX 2 AA2 THR A 33 ASP A 63 1 31 HELIX 3 AA3 ASP A 67 ALA A 94 1 28 HELIX 4 AA4 HIS B -1 GLY B 31 1 33 HELIX 5 AA5 THR B 33 ASP B 63 1 31 HELIX 6 AA6 ASP B 67 ALA B 94 1 28 CRYST1 72.719 37.286 83.821 90.00 106.83 90.00 I 1 2 1 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 0.013752 0.000000 0.004160 0.00000 SCALE2 0.000000 0.026820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012464 0.00000 MASTER 330 0 0 6 0 0 0 6 1495 2 0 18 END