HEADER DE NOVO PROTEIN 17-OCT-22 8BCS TITLE X-RAY CRYSTAL STRUCTURE OF A DE NOVO DESIGNED HELIX-LOOP-HELIX TITLE 2 HOMODIMER IN AN ANTI ARRANGEMENT, CC-HP1.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CC-HP1.0; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS COILED COIL, 4-HELIX BUNDLE, DE NOVO PROTEIN DESIGN, HELIX-LOOP-HELIX KEYWDS 2 DIMER, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.L.EDGELL,B.MYLEMANS,E.A.NAUDIN,A.J.SMITH,N.J.SAVERY,D.N.WOOLFSON REVDAT 3 07-FEB-24 8BCS 1 REMARK REVDAT 2 28-JUN-23 8BCS 1 JRNL REVDAT 1 07-JUN-23 8BCS 0 JRNL AUTH A.J.SMITH,E.A.NAUDIN,C.L.EDGELL,E.G.BAKER,B.MYLEMANS, JRNL AUTH 2 L.FITZPATRICK,A.HERMAN,H.M.RICE,D.M.ANDREWS,N.TIGUE, JRNL AUTH 3 D.N.WOOLFSON,N.J.SAVERY JRNL TITL DESIGN AND SELECTION OF HETERODIMERIZING HELICAL HAIRPINS JRNL TITL 2 FOR SYNTHETIC BIOLOGY. JRNL REF ACS SYNTH BIOL V. 12 1845 2023 JRNL REFN ESSN 2161-5063 JRNL PMID 37224449 JRNL DOI 10.1021/ACSSYNBIO.3C00231 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 2895 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.250 REMARK 3 FREE R VALUE TEST SET COUNT : 152 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 31.5600 - 3.5900 1.00 593 34 0.1943 0.1800 REMARK 3 2 3.5900 - 2.8500 1.00 550 30 0.2663 0.3544 REMARK 3 3 2.8500 - 2.4900 1.00 520 39 0.3457 0.4161 REMARK 3 4 2.4900 - 2.2600 1.00 549 21 0.3389 0.4511 REMARK 3 5 2.2600 - 2.1000 1.00 531 28 0.3346 0.3856 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) : 0.235 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.823 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.81 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 : 0.008 331 REMARK 3 ANGLE : 0.988 449 REMARK 3 CHIRALITY : 0.046 59 REMARK 3 PLANARITY : 0.004 56 REMARK 3 DIHEDRAL : 19.600 108 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 49 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.2379 -7.9973 4.1898 REMARK 3 T TENSOR REMARK 3 T11: 0.4835 T22: 0.6192 REMARK 3 T33: 0.3916 T12: -0.0375 REMARK 3 T13: 0.0337 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 7.7673 L22: 8.1096 REMARK 3 L33: 5.5061 L12: -1.6101 REMARK 3 L13: -2.6978 L23: 2.2068 REMARK 3 S TENSOR REMARK 3 S11: -0.0924 S12: -1.0956 S13: -0.2736 REMARK 3 S21: 0.4017 S22: 0.5497 S23: 0.5141 REMARK 3 S31: -0.3351 S32: 1.1766 S33: -0.4839 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 8BCS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : 3400 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 31.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 16.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: 6Q5S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 SODIUM CACODYLATE, 30% W/V PEG 8000, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.77633 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.55267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.55267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.77633 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ACE A 0 REMARK 465 NH2 A 50 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 GLU A 2 CD OE1 OE2 REMARK 470 GLU A 4 CG CD OE1 OE2 REMARK 470 LYS A 8 CD CE NZ REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 LYS A 11 CE NZ REMARK 470 LYS A 18 CE NZ REMARK 470 LYS A 22 CD CE NZ REMARK 470 GLN A 27 CG CD OE1 NE2 REMARK 470 GLU A 30 CD OE1 OE2 REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 LYS A 42 CG CD CE NZ REMARK 470 LYS A 44 CE NZ REMARK 470 GLN A 48 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 23 57.92 -143.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BCS A 0 50 PDB 8BCS 8BCS 0 50 SEQRES 1 A 51 ACE GLY GLU LEU GLU ALA LEU ALA LYS LYS LEU LYS ALA SEQRES 2 A 51 LEU ALA TRP LYS LEU LYS ALA LEU SER LYS GLU PRO SER SEQRES 3 A 51 ALA GLN GLU LEU GLU ALA LEU ALA GLN GLU LEU GLU ALA SEQRES 4 A 51 LEU ALA LYS LYS LEU LYS ALA LEU ALA GLN GLY NH2 HET ACT A 101 4 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- HELIX 1 AA1 GLY A 1 SER A 21 1 21 HELIX 2 AA2 SER A 25 GLY A 49 1 25 CRYST1 36.438 36.438 59.329 90.00 90.00 120.00 P 31 2 1 6 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 0.027444 0.015845 0.000000 0.00000 SCALE2 0.000000 0.031689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016855 0.00000