HEADER DE NOVO PROTEIN 23-MAR-15 4YXZ TITLE COMPUTATIONALLY DESIGNED LEFT-HANDED ALPHA/ALPHA TOROID WITH 9 REPEATS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DTOR_9X31L; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DTOR_9X31L; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: ROSETTA DESIGNED KEYWDS ROSETTA, TOROID, ALPHA HELIX, COMPUTATIONALLY DESIGNED, LEFT-HANDED, KEYWDS 2 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.DOYLE,B.L.STODDARD,P.BRADLEY REVDAT 7 06-MAR-24 4YXZ 1 REMARK REVDAT 6 25-DEC-19 4YXZ 1 REMARK REVDAT 5 22-NOV-17 4YXZ 1 REMARK REVDAT 4 06-SEP-17 4YXZ 1 JRNL REMARK REVDAT 3 06-JAN-16 4YXZ 1 JRNL REVDAT 2 30-DEC-15 4YXZ 1 JRNL REVDAT 1 16-DEC-15 4YXZ 0 JRNL AUTH L.DOYLE,J.HALLINAN,J.BOLDUC,F.PARMEGGIANI,D.BAKER, JRNL AUTH 2 B.L.STODDARD,P.BRADLEY JRNL TITL RATIONAL DESIGN OF ALPHA-HELICAL TANDEM REPEAT PROTEINS WITH JRNL TITL 2 CLOSED ARCHITECTURES. JRNL REF NATURE V. 528 585 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26675735 JRNL DOI 10.1038/NATURE16191 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 9355 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.328 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 936 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 29.9822 - 4.7691 0.99 1297 144 0.2070 0.2935 REMARK 3 2 4.7691 - 3.7878 0.99 1217 135 0.1932 0.3005 REMARK 3 3 3.7878 - 3.3097 1.00 1225 136 0.2166 0.3022 REMARK 3 4 3.3097 - 3.0074 0.99 1192 130 0.2724 0.3901 REMARK 3 5 3.0074 - 2.7920 0.98 1177 133 0.2503 0.3566 REMARK 3 6 2.7920 - 2.6275 0.99 1189 133 0.2723 0.3906 REMARK 3 7 2.6275 - 2.4960 0.94 1122 125 0.2445 0.3750 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.74 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 2037 REMARK 3 ANGLE : 1.038 2779 REMARK 3 CHIRALITY : 0.035 350 REMARK 3 PLANARITY : 0.004 339 REMARK 3 DIHEDRAL : 14.834 683 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4YXZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208119. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9450 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.496 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.25800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: COMPUTATIONALLY DESIGNED MOLECULE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 1.0 M AMMONIUM REMARK 280 PHOSPHATE MONOBASIC, PH 5.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 20.86800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.09300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.00950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.09300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.86800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.00950 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 2 REMARK 465 SER A 3 REMARK 465 MET A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 286 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 LYS A 18 CE NZ REMARK 470 THR A 26 OG1 CG2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 LEU A 35 CG CD1 CD2 REMARK 470 LYS A 36 CE NZ REMARK 470 ILE A 39 CG1 CG2 CD1 REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 VAL A 58 CG1 CG2 REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LEU A 66 CD1 CD2 REMARK 470 LYS A 67 CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LEU A 97 CG CD1 CD2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 LEU A 128 CD1 CD2 REMARK 470 LYS A 129 CD CE NZ REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 ILE A 163 CG1 CG2 CD1 REMARK 470 LYS A 170 CD CE NZ REMARK 470 LYS A 173 CE NZ REMARK 470 THR A 181 OG1 CG2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 ILE A 194 CG1 CG2 CD1 REMARK 470 LYS A 201 CE NZ REMARK 470 LYS A 204 NZ REMARK 470 LYS A 222 CE NZ REMARK 470 LYS A 232 CE NZ REMARK 470 LYS A 249 CD CE NZ REMARK 470 LYS A 253 CD CE NZ REMARK 470 LYS A 263 NZ REMARK 470 LYS A 266 NZ REMARK 470 LYS A 284 CG CD CE NZ 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 LYS A 98 11.02 -59.85 REMARK 500 LEU A 99 -6.93 -141.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 4YXZ A 1 286 PDB 4YXZ 4YXZ 1 286 SEQRES 1 A 286 GLY SER SER MET ALA SER GLY ILE SER VAL GLU GLU LEU SEQRES 2 A 286 LEU LYS LEU ALA LYS ALA ALA TYR TYR SER GLY THR THR SEQRES 3 A 286 VAL GLU GLU ALA TYR LYS LEU ALA LEU LYS LEU GLY ILE SEQRES 4 A 286 SER VAL GLU GLU LEU LEU LYS LEU ALA GLU ALA ALA TYR SEQRES 5 A 286 TYR SER GLY THR THR VAL GLU GLU ALA TYR LYS LEU ALA SEQRES 6 A 286 LEU LYS LEU GLY ILE SER VAL GLU GLU LEU LEU LYS LEU SEQRES 7 A 286 ALA LYS ALA ALA TYR TYR SER GLY THR THR VAL GLU GLU SEQRES 8 A 286 ALA TYR LYS LEU ALA LEU LYS LEU GLY ILE SER VAL GLU SEQRES 9 A 286 GLU LEU LEU LYS LEU ALA LYS ALA ALA TYR TYR SER GLY SEQRES 10 A 286 THR THR VAL GLU GLU ALA TYR LYS LEU ALA LEU LYS LEU SEQRES 11 A 286 GLY ILE SER VAL GLU GLU LEU LEU LYS LEU ALA GLU ALA SEQRES 12 A 286 ALA TYR TYR SER GLY THR THR VAL GLU GLU ALA TYR LYS SEQRES 13 A 286 LEU ALA LEU LYS LEU GLY ILE SER VAL GLU GLU LEU LEU SEQRES 14 A 286 LYS LEU ALA LYS ALA ALA TYR TYR SER GLY THR THR VAL SEQRES 15 A 286 GLU GLU ALA TYR LYS LEU ALA LEU LYS LEU GLY ILE SER SEQRES 16 A 286 VAL GLU GLU LEU LEU LYS LEU ALA LYS ALA ALA TYR TYR SEQRES 17 A 286 SER GLY THR THR VAL GLU GLU ALA TYR LYS LEU ALA LEU SEQRES 18 A 286 LYS LEU GLY ILE SER VAL GLU GLU LEU LEU LYS LEU ALA SEQRES 19 A 286 GLU ALA ALA TYR TYR SER GLY THR THR VAL GLU GLU ALA SEQRES 20 A 286 TYR LYS LEU ALA LEU LYS LEU GLY ILE SER VAL GLU GLU SEQRES 21 A 286 LEU LEU LYS LEU ALA LYS ALA ALA TYR TYR SER GLY THR SEQRES 22 A 286 THR VAL GLU GLU ALA TYR LYS LEU ALA LEU LYS LEU GLY HELIX 1 AA1 SER A 9 GLY A 24 1 16 HELIX 2 AA2 THR A 26 LEU A 37 1 12 HELIX 3 AA3 SER A 40 GLY A 55 1 16 HELIX 4 AA4 THR A 57 GLY A 69 1 13 HELIX 5 AA5 SER A 71 GLY A 86 1 16 HELIX 6 AA6 THR A 88 LYS A 98 1 11 HELIX 7 AA7 SER A 102 GLY A 117 1 16 HELIX 8 AA8 THR A 119 GLY A 131 1 13 HELIX 9 AA9 SER A 133 GLY A 148 1 16 HELIX 10 AB1 THR A 150 LEU A 161 1 12 HELIX 11 AB2 SER A 164 GLY A 179 1 16 HELIX 12 AB3 THR A 181 LEU A 192 1 12 HELIX 13 AB4 SER A 195 GLY A 210 1 16 HELIX 14 AB5 THR A 212 LEU A 223 1 12 HELIX 15 AB6 SER A 226 GLY A 241 1 16 HELIX 16 AB7 THR A 243 LEU A 254 1 12 HELIX 17 AB8 SER A 257 GLY A 272 1 16 HELIX 18 AB9 THR A 274 LEU A 285 1 12 CRYST1 41.736 72.019 86.186 90.00 90.00 90.00 P 21 21 21 4 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 0.023960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011603 0.00000