HEADER DE NOVO PROTEIN 20-OCT-21 7Q1T TITLE A DE NOVO DESIGNED HETERO-DIMERIC ANTIPARALLEL COILED COIL APCC-DI-AB COMPND MOL_ID: 1; COMPND 2 MOLECULE: APCC-DI-A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: APCC-DI-B; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS ANTIPARALLEL, HETERO-DIMERIC, COILED-COIL, DE NOVO, PROTEIN DESIGN, KEYWDS 2 ASSOCIATING PEPTIDES, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SHANMUGARATNAM,G.G.RHYS,W.M.DAWSON,D.N.WOOLFSON,B.HOCKER REVDAT 4 01-MAY-24 7Q1T 1 REMARK REVDAT 3 31-AUG-22 7Q1T 1 JRNL REVDAT 2 27-JUL-22 7Q1T 1 JRNL REVDAT 1 20-JUL-22 7Q1T 0 JRNL AUTH G.G.RHYS,J.A.CROSS,W.M.DAWSON,H.F.THOMPSON,S.SHANMUGARATNAM, JRNL AUTH 2 N.J.SAVERY,M.P.DODDING,B.HOCKER,D.N.WOOLFSON JRNL TITL DE NOVO DESIGNED PEPTIDES FOR CELLULAR DELIVERY AND JRNL TITL 2 SUBCELLULAR LOCALISATION. JRNL REF NAT.CHEM.BIOL. V. 18 999 2022 JRNL REFN ESSN 1552-4469 JRNL PMID 35836017 JRNL DOI 10.1038/S41589-022-01076-6 REMARK 2 REMARK 2 RESOLUTION. 1.68 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 8646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.480 REMARK 3 FREE R VALUE TEST SET COUNT : 906 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 24.1900 - 3.0500 0.98 1299 159 0.1607 0.2039 REMARK 3 2 3.0500 - 2.4200 0.98 1281 149 0.1871 0.2045 REMARK 3 3 2.4200 - 2.1200 1.00 1308 149 0.1906 0.2172 REMARK 3 4 2.1200 - 1.9200 0.98 1277 146 0.2182 0.2553 REMARK 3 5 1.9200 - 1.7900 0.99 1305 149 0.2618 0.2971 REMARK 3 6 1.7900 - 1.6800 0.97 841 89 0.3530 0.3847 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) : 0.252 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.03 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 : 0.002 509 REMARK 3 ANGLE : 0.322 681 REMARK 3 CHIRALITY : 0.023 72 REMARK 3 PLANARITY : 0.002 91 REMARK 3 DIHEDRAL : 18.396 204 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 30) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0272 -4.9867 9.1030 REMARK 3 T TENSOR REMARK 3 T11: 0.3245 T22: 0.2231 REMARK 3 T33: 0.2293 T12: -0.0626 REMARK 3 T13: -0.0245 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.7781 L22: 1.3276 REMARK 3 L33: 2.7579 L12: -0.2081 REMARK 3 L13: -0.3100 L23: -0.2470 REMARK 3 S TENSOR REMARK 3 S11: 0.2984 S12: 0.2702 S13: 0.1308 REMARK 3 S21: -0.3154 S22: -0.1821 S23: 0.0192 REMARK 3 S31: 0.2708 S32: -0.0964 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 30) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3029 -9.4654 16.8241 REMARK 3 T TENSOR REMARK 3 T11: 0.3433 T22: 0.2586 REMARK 3 T33: 0.2726 T12: -0.0806 REMARK 3 T13: -0.0220 T23: 0.0536 REMARK 3 L TENSOR REMARK 3 L11: 0.7606 L22: 2.8198 REMARK 3 L33: 3.2767 L12: -1.2291 REMARK 3 L13: -0.5704 L23: -0.1986 REMARK 3 S TENSOR REMARK 3 S11: -0.0349 S12: 0.0483 S13: -0.3977 REMARK 3 S21: -0.2679 S22: 0.1573 S23: 0.2493 REMARK 3 S31: 0.2850 S32: 0.0864 S33: 0.0004 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 7Q1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DCM SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 2.0.2 REMARK 200 DATA SCALING SOFTWARE : DIALS 2.0.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8726 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 24.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.41500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 1.58700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: POLY-ALANINE COILED-COIL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 0.1M PHOSPHATE REMARK 280 CITRATE PH 4.2, 10% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 23.60950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 23.60950 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.08450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.60950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.54225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.60950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.62675 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.60950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.60950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.08450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 23.60950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.62675 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 23.60950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 17.54225 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: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 127 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 247 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 119 O HOH B 241 7454 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 A 125 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 126 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 127 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A 128 DISTANCE = 10.30 ANGSTROMS REMARK 525 HOH B 244 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B 245 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH B 246 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH B 247 DISTANCE = 8.52 ANGSTROMS DBREF 7Q1T A 1 30 PDB 7Q1T 7Q1T 1 30 DBREF 7Q1T B 1 30 PDB 7Q1T 7Q1T 1 30 SEQRES 1 A 30 GLY GLN LEU GLU GLN GLU LEU ALA ALA LEU ASP GLN GLU SEQRES 2 A 30 ILE ALA ALA ALA GLU GLN GLU LEU ALA ALA LEU ASP TRP SEQRES 3 A 30 GLN ILE GLN GLY SEQRES 1 B 30 GLY GLN LEU LYS GLN ARG ARG ALA ALA LEU LYS GLN ARG SEQRES 2 B 30 ILE ALA ALA LEU LYS GLN ARG ARG ALA ALA LEU LYS TRP SEQRES 3 B 30 GLN ILE GLN GLY HET POL B 101 12 HET POL B 102 12 HET SO4 B 103 5 HETNAM POL N-PROPANOL HETNAM SO4 SULFATE ION HETSYN POL 1-PROPONOL FORMUL 3 POL 2(C3 H8 O) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *75(H2 O) HELIX 1 AA1 GLY A 1 GLN A 29 1 29 HELIX 2 AA2 GLN B 2 GLY B 30 1 29 CRYST1 47.219 47.219 70.169 90.00 90.00 90.00 I 41 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 0.021178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014251 0.00000 CONECT 1011 1012 1015 CONECT 1012 1011 1013 1016 1017 CONECT 1013 1012 1014 1018 1019 CONECT 1014 1013 1020 1021 1022 CONECT 1015 1011 CONECT 1016 1012 CONECT 1017 1012 CONECT 1018 1013 CONECT 1019 1013 CONECT 1020 1014 CONECT 1021 1014 CONECT 1022 1014 CONECT 1023 1024 1027 CONECT 1024 1023 1025 1028 1029 CONECT 1025 1024 1026 1030 1031 CONECT 1026 1025 1032 1033 1034 CONECT 1027 1023 CONECT 1028 1024 CONECT 1029 1024 CONECT 1030 1025 CONECT 1031 1025 CONECT 1032 1026 CONECT 1033 1026 CONECT 1034 1026 CONECT 1035 1036 1037 1038 1039 CONECT 1036 1035 CONECT 1037 1035 CONECT 1038 1035 CONECT 1039 1035 MASTER 292 0 3 2 0 0 0 6 562 2 29 6 END