HEADER DE NOVO PROTEIN 19-DEC-22 8FJF TITLE THE THREE-REPEAT DESIGN H10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: H10; COMPND 3 CHAIN: A; 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 8FJF 1 JRNL REVDAT 3 11-OCT-23 8FJF 1 JRNL REVDAT 2 04-OCT-23 8FJF 1 TITLE JRNL REVDAT 1 27-SEP-23 8FJF 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 30089 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1555 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 38.5300 - 3.5600 1.00 2608 136 0.1436 0.1771 REMARK 3 2 3.5500 - 2.8200 1.00 2567 160 0.1923 0.2213 REMARK 3 3 2.8200 - 2.4700 1.00 2593 133 0.2313 0.2416 REMARK 3 4 2.4700 - 2.2400 1.00 2608 143 0.2302 0.2424 REMARK 3 5 2.2400 - 2.0800 1.00 2573 153 0.2280 0.2697 REMARK 3 6 2.0800 - 1.9600 1.00 2629 124 0.2364 0.2825 REMARK 3 7 1.9600 - 1.8600 1.00 2564 164 0.2611 0.3415 REMARK 3 8 1.8600 - 1.7800 1.00 2599 129 0.2395 0.2531 REMARK 3 9 1.7800 - 1.7100 1.00 2611 137 0.2802 0.3196 REMARK 3 10 1.7100 - 1.6500 1.00 2633 132 0.3150 0.3466 REMARK 3 11 1.6500 - 1.6000 0.99 2549 144 0.3403 0.3688 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) : 0.232 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.97 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 : 0.011 995 REMARK 3 ANGLE : 1.049 1337 REMARK 3 CHIRALITY : 0.073 149 REMARK 3 PLANARITY : 0.007 171 REMARK 3 DIHEDRAL : 12.757 375 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): 1.1787 -2.6445 -10.2158 REMARK 3 T TENSOR REMARK 3 T11: 0.1962 T22: 0.2445 REMARK 3 T33: 0.2339 T12: 0.0055 REMARK 3 T13: 0.0196 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 1.0384 L22: 3.2666 REMARK 3 L33: 2.4688 L12: -0.5796 REMARK 3 L13: 1.2035 L23: -0.6256 REMARK 3 S TENSOR REMARK 3 S11: -0.1274 S12: -0.1052 S13: 0.0408 REMARK 3 S21: 0.1378 S22: 0.0172 S23: 0.0429 REMARK 3 S31: -0.1329 S32: -0.0629 S33: -0.0091 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 8FJF 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_1000270899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-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) : 0.97926 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 : 30089 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : 1.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.970 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 (%): 39.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12 M D-GLUCOSE, 0.12 M D-MANNOSE, REMARK 280 0.12 M D-GALACTOSE, 0.12 M L-FUCOSE, 0.12 M D-XYLOSE, 0.12 M N- REMARK 280 ACETYL-D-GLUCOSAMINE, 0.0499 M HEPES, 0.0501 M MOPS (ACID), 20% REMARK 280 V/V PEG 500 MME, AND 10% W/V PEG 20,000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 17.00200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.06150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.14350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.06150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.00200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.14350 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 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 SER A -1 REMARK 465 GLY A 0 REMARK 465 PRO A 128 REMARK 465 ALA A 129 REMARK 465 GLY A 130 REMARK 465 SER A 131 REMARK 465 GLY A 132 DBREF 8FJF A -1 132 PDB 8FJF 8FJF -1 132 SEQRES 1 A 134 SER GLY SER LYS TYR VAL VAL ILE ASP GLY GLU GLY ASN SEQRES 2 A 134 GLU TYR GLU PHE THR ASP LEU LYS GLU ALA ALA ALA LYS SEQRES 3 A 134 ALA LYS GLU LEU LYS LYS LYS TYR GLY PHE ALA SER ILE SEQRES 4 A 134 SER VAL PRO VAL GLU PRO ASP GLU VAL ALA VAL VAL ASP SEQRES 5 A 134 GLY LYS GLY ASN GLU HIS THR PHE THR ASP ILE LYS LYS SEQRES 6 A 134 ALA VAL GLU LYS ALA LYS GLU LEU ALA LYS GLU THR GLY SEQRES 7 A 134 PHE ALA SER ILE SER VAL PRO VAL GLU PRO ASP GLU TYR SEQRES 8 A 134 LEU VAL ILE ASP GLY LYS GLY ASN GLU HIS LYS PHE THR SEQRES 9 A 134 ASP LEU LYS GLU ALA VAL ALA LYS ALA LYS GLU LEU LYS SEQRES 10 A 134 LYS LYS TYR GLY PHE ALA SER VAL SER VAL PRO VAL PRO SEQRES 11 A 134 ALA GLY SER GLY FORMUL 2 HOH *62(H2 O) HELIX 1 AA1 ASP A 17 GLY A 33 1 17 HELIX 2 AA2 ASP A 60 GLY A 76 1 17 HELIX 3 AA3 ASP A 103 GLY A 119 1 17 SHEET 1 AA1 3 GLU A 12 PHE A 15 0 SHEET 2 AA1 3 TYR A 3 ASP A 7 -1 N VAL A 5 O TYR A 13 SHEET 3 AA1 3 ALA A 35 SER A 38 -1 O SER A 38 N VAL A 4 SHEET 1 AA2 3 GLU A 55 PHE A 58 0 SHEET 2 AA2 3 VAL A 46 ASP A 50 -1 N VAL A 48 O HIS A 56 SHEET 3 AA2 3 ALA A 78 SER A 81 -1 O SER A 81 N ALA A 47 SHEET 1 AA3 3 GLU A 98 PHE A 101 0 SHEET 2 AA3 3 TYR A 89 ASP A 93 -1 N TYR A 89 O PHE A 101 SHEET 3 AA3 3 ALA A 121 SER A 124 -1 O SER A 124 N LEU A 90 CRYST1 34.004 44.287 78.123 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 0.029408 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012800 0.00000