HEADER DE NOVO PROTEIN 19-DEC-22 8FJE TITLE THE FIVE-REPEAT DESIGN E8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E8; 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 DE NOVO PROTEIN, HALLUCINATION, REPEAT PROTEINS, CENTRAL POCKETS, KEYWDS 2 PSEUDOCYCLIC PROTEINS EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,L.AN,D.BAKER REVDAT 4 22-NOV-23 8FJE 1 JRNL REVDAT 3 11-OCT-23 8FJE 1 JRNL REVDAT 2 04-OCT-23 8FJE 1 TITLE JRNL REVDAT 1 27-SEP-23 8FJE 0 JRNL AUTH L.AN,D.R.HICKS,D.ZORINE,J.DAUPARAS,B.I.M.WICKY,L.F.MILLES, JRNL AUTH 2 A.COURBET,A.K.BERA,H.NGUYEN,A.KANG,L.CARTER,D.BAKER JRNL TITL HALLUCINATION OF CLOSED REPEAT PROTEINS CONTAINING CENTRAL JRNL TITL 2 POCKETS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 1755 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 37770718 JRNL DOI 10.1038/S41594-023-01112-6 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 5818 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.271 REMARK 3 R VALUE (WORKING SET) : 0.267 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 570 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 52.5600 - 4.7600 0.98 1372 152 0.2473 0.2354 REMARK 3 2 4.7600 - 3.7800 0.98 1301 152 0.2657 0.3782 REMARK 3 3 3.7800 - 3.3000 0.99 1261 152 0.2957 0.3728 REMARK 3 4 3.3000 - 3.0000 1.00 1314 114 0.3241 0.3636 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) : 0.398 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.025 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.70 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 2354 REMARK 3 ANGLE : 0.437 3174 REMARK 3 CHIRALITY : 0.032 340 REMARK 3 PLANARITY : 0.004 420 REMARK 3 DIHEDRAL : 3.463 320 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.7324 17.4947 20.1120 REMARK 3 T TENSOR REMARK 3 T11: 0.4487 T22: 0.3663 REMARK 3 T33: 0.4371 T12: 0.0187 REMARK 3 T13: -0.0100 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 1.1080 L22: 0.1184 REMARK 3 L33: 3.5294 L12: 0.2497 REMARK 3 L13: -0.2415 L23: 0.2836 REMARK 3 S TENSOR REMARK 3 S11: 0.1274 S12: -0.0885 S13: -0.1172 REMARK 3 S21: 0.1275 S22: -0.1993 S23: -0.0625 REMARK 3 S31: -0.1506 S32: -0.2308 S33: 0.0000 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 8FJE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5818 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 52.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.20300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : 1.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.480 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 (%): 38.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M DL-GLUTAMIC ACID MONOHYDRATE, REMARK 280 0.2M, DL-ALANINE, 0.2M GLYCINE, 0.2M DL-LYSINE, 1.0M IMIDAZOLE, REMARK 280 MES MONOHYDRATE (ACID), 37.5 % V/V OF (25% V/V MPD; 25% PEG 1000; REMARK 280 25% W/V PEG 3350), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.88150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.71700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.88150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.71700 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: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 SER A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 SER A 140 REMARK 465 GLY A 141 REMARK 465 SER A 142 REMARK 465 GLY A 143 REMARK 465 SER B -1 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 PRO B 2 REMARK 465 THR B 3 REMARK 465 SER B 140 REMARK 465 GLY B 141 REMARK 465 SER B 142 REMARK 465 GLY B 143 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 ARG A 24 -66.78 -98.10 REMARK 500 GLU A 34 11.54 -142.70 REMARK 500 THR B 55 95.17 -64.68 REMARK 500 ARG B 108 -71.98 -73.18 REMARK 500 SER B 111 34.15 -87.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FJE A -1 143 PDB 8FJE 8FJE -1 143 DBREF 8FJE B -1 143 PDB 8FJE 8FJE -1 143 SEQRES 1 A 145 SER GLY SER PRO THR PRO LEU GLU THR LEU PRO LEU GLU SEQRES 2 A 145 GLU LEU GLU ARG ARG ALA LEU LYS ILE TYR LEU ARG ARG SEQRES 3 A 145 HIS GLY SER VAL PRO GLU GLU GLU ILE GLU THR MET PRO SEQRES 4 A 145 LEU GLU GLU LEU GLU ARG LYS ALA LEU GLN ASP TYR LEU SEQRES 5 A 145 ARG ARG TYR GLY THR LEU PRO GLU GLU GLU ILE GLU THR SEQRES 6 A 145 MET PRO LEU GLU GLU LEU GLU ARG GLU ALA LEU LYS ASN SEQRES 7 A 145 TYR LEU ARG ARG TYR GLY THR LEU PRO GLU GLU GLU ILE SEQRES 8 A 145 ASP THR MET PRO LEU GLU GLU LEU GLU ARG GLU ALA LEU SEQRES 9 A 145 LYS ASN TYR LEU ARG ARG TYR GLY SER LEU PRO PRO GLU SEQRES 10 A 145 GLU LEU GLU LYS LEU PRO LEU GLU GLU LEU GLU ARG LYS SEQRES 11 A 145 ALA LEU ILE GLU TYR LEU ARG ARG TYR GLY PRO SER GLY SEQRES 12 A 145 SER GLY SEQRES 1 B 145 SER GLY SER PRO THR PRO LEU GLU THR LEU PRO LEU GLU SEQRES 2 B 145 GLU LEU GLU ARG ARG ALA LEU LYS ILE TYR LEU ARG ARG SEQRES 3 B 145 HIS GLY SER VAL PRO GLU GLU GLU ILE GLU THR MET PRO SEQRES 4 B 145 LEU GLU GLU LEU GLU ARG LYS ALA LEU GLN ASP TYR LEU SEQRES 5 B 145 ARG ARG TYR GLY THR LEU PRO GLU GLU GLU ILE GLU THR SEQRES 6 B 145 MET PRO LEU GLU GLU LEU GLU ARG GLU ALA LEU LYS ASN SEQRES 7 B 145 TYR LEU ARG ARG TYR GLY THR LEU PRO GLU GLU GLU ILE SEQRES 8 B 145 ASP THR MET PRO LEU GLU GLU LEU GLU ARG GLU ALA LEU SEQRES 9 B 145 LYS ASN TYR LEU ARG ARG TYR GLY SER LEU PRO PRO GLU SEQRES 10 B 145 GLU LEU GLU LYS LEU PRO LEU GLU GLU LEU GLU ARG LYS SEQRES 11 B 145 ALA LEU ILE GLU TYR LEU ARG ARG TYR GLY PRO SER GLY SEQRES 12 B 145 SER GLY HELIX 1 AA1 PRO A 4 LEU A 8 5 5 HELIX 2 AA2 PRO A 9 HIS A 25 1 17 HELIX 3 AA3 PRO A 37 TYR A 53 1 17 HELIX 4 AA4 PRO A 57 GLU A 62 1 6 HELIX 5 AA5 PRO A 65 GLY A 82 1 18 HELIX 6 AA6 PRO A 85 MET A 92 1 8 HELIX 7 AA7 PRO A 93 TYR A 109 1 17 HELIX 8 AA8 PRO A 113 LEU A 120 1 8 HELIX 9 AA9 PRO A 121 GLY A 138 1 18 HELIX 10 AB1 PRO B 4 LEU B 8 5 5 HELIX 11 AB2 PRO B 9 HIS B 25 1 17 HELIX 12 AB3 PRO B 37 GLY B 54 1 18 HELIX 13 AB4 GLU B 59 MET B 64 1 6 HELIX 14 AB5 PRO B 65 GLY B 82 1 18 HELIX 15 AB6 GLU B 86 MET B 92 1 7 HELIX 16 AB7 PRO B 93 TYR B 109 1 17 HELIX 17 AB8 PRO B 113 LEU B 120 1 8 HELIX 18 AB9 PRO B 121 GLY B 138 1 18 CRYST1 47.859 65.763 87.434 90.00 90.00 90.00 P 2 21 21 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 0.020895 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015206 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011437 0.00000