HEADER DE NOVO PROTEIN 27-NOV-21 7QDJ TITLE RACEMIC STRUCTURE OF PK-10 AND PK-11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PK-10+PK-11; 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 ALPHA-HELICAL, RACEMIC STRUCTURE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.KUMAR,N.G.PATERSON,D.N.WOOLFSON REVDAT 4 27-JUL-22 7QDJ 1 JRNL REVDAT 3 06-JUL-22 7QDJ 1 JRNL REVDAT 2 29-JUN-22 7QDJ 1 JRNL REVDAT 1 27-APR-22 7QDJ 0 JRNL AUTH P.KUMAR,N.G.PATERSON,J.CLAYDEN,D.N.WOOLFSON JRNL TITL DE NOVO DESIGN OF DISCRETE, STABLE 3 10 -HELIX PEPTIDE JRNL TITL 2 ASSEMBLIES. JRNL REF NATURE V. 607 387 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35732733 JRNL DOI 10.1038/S41586-022-04868-X REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 4677 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 230 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 351 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.1500 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.1940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 145 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.25000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.051 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.187 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 175 ; 0.026 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 186 ; 0.004 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 244 ; 3.229 ; 1.658 REMARK 3 BOND ANGLES OTHERS (DEGREES): 413 ; 1.463 ; 1.589 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 22 ; 4.561 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 4 ;28.246 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 26 ; 9.514 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 11 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 628 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 100 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 358 ; 4.807 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 20 REMARK 3 ORIGIN FOR THE GROUP (A): 4.3349 0.9944 2.6809 REMARK 3 T TENSOR REMARK 3 T11: 0.0075 T22: 0.0024 REMARK 3 T33: 0.0012 T12: -0.0014 REMARK 3 T13: -0.0008 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.8271 L22: 3.0876 REMARK 3 L33: 7.3728 L12: -1.5635 REMARK 3 L13: -2.0332 L23: 3.5210 REMARK 3 S TENSOR REMARK 3 S11: -0.0524 S12: -0.0455 S13: 0.0251 REMARK 3 S21: 0.0703 S22: 0.0293 S23: 0.0152 REMARK 3 S31: -0.0520 S32: 0.1032 S33: 0.0232 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7QDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9119 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5150 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 27.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 0.09700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M (SODIUM MALONATE DIBASIC REMARK 280 MONOHYDRATE, IMIDAZOLE, BORIC ACID), 25% W/V PEG1500 AT PH 7.0, REMARK 280 PH 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2/c 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z+1/2 REMARK 290 3555 -X,-Y,-Z REMARK 290 4555 X,-Y,Z+1/2 REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 7555 -X+1/2,-Y+1/2,-Z REMARK 290 8555 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 -3.20261 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 27.63706 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 -3.20261 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.63706 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 13.46400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 9.68950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 10.26139 REMARK 290 SMTRY2 6 0.000000 1.000000 0.000000 9.68950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.63706 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 13.46400 REMARK 290 SMTRY2 7 0.000000 -1.000000 0.000000 9.68950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 10.26139 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 9.68950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 27.63706 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: 330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 C1 MLI A 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 219 LIES ON A SPECIAL POSITION. DBREF 7QDJ A 0 20 PDB 7QDJ 7QDJ 0 20 SEQRES 1 A 21 ACE GLY GLU LEU AIB AIB LEU LYS GLU LEU AIB AIB LEU SEQRES 2 A 21 LYS AIB AIB AIB TRP LYS GLY NH2 HET ACE A 0 3 HET AIB A 4 6 HET AIB A 5 6 HET AIB A 10 6 HET AIB A 11 6 HET AIB A 14 6 HET AIB A 15 6 HET AIB A 16 6 HET NH2 A 20 1 HET MLI A 101 7 HET GOL A 102 6 HET NA A 103 1 HET NA A 104 1 HETNAM ACE ACETYL GROUP HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM NH2 AMINO GROUP HETNAM MLI MALONATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 ACE C2 H4 O FORMUL 1 AIB 7(C4 H9 N O2) FORMUL 1 NH2 H2 N FORMUL 2 MLI C3 H2 O4 2- FORMUL 3 GOL C3 H8 O3 FORMUL 4 NA 2(NA 1+) FORMUL 6 HOH *27(H2 O) HELIX 1 AA1 GLY A 1 GLY A 19 1 19 LINK C ACE A 0 N GLY A 1 1555 1555 1.35 LINK C LEU A 3 N AIB A 4 1555 1555 1.33 LINK C AIB A 4 N AIB A 5 1555 1555 1.32 LINK C AIB A 5 N LEU A 6 1555 1555 1.32 LINK C LEU A 9 N AIB A 10 1555 1555 1.32 LINK C AIB A 10 N AIB A 11 1555 1555 1.33 LINK C AIB A 11 N LEU A 12 1555 1555 1.32 LINK C LYS A 13 N AIB A 14 1555 1555 1.35 LINK C AIB A 14 N AIB A 15 1555 1555 1.33 LINK C AIB A 15 N AIB A 16 1555 1555 1.34 LINK C AIB A 16 N TRP A 17 1555 1555 1.33 LINK C BGLY A 19 N NH2 A 20 1555 1555 1.36 CRYST1 26.928 19.379 55.644 90.00 96.61 90.00 C 1 2/c 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 0.037136 0.000000 0.004302 0.00000 SCALE2 0.000000 0.051602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018092 0.00000 HETATM 1 C ACE A 0 7.224 -4.634 -9.994 1.00 6.51 C ANISOU 1 C ACE A 0 946 1041 487 111 200 48 C HETATM 2 O ACE A 0 7.417 -4.049 -8.958 1.00 6.75 O ANISOU 2 O ACE A 0 938 1090 536 79 73 -73 O HETATM 3 CH3 ACE A 0 8.294 -5.328 -10.751 1.00 7.87 C ANISOU 3 CH3 ACE A 0 1025 1334 629 45 250 -211 C