HEADER DE NOVO PROTEIN 19-DEC-22 8FJG TITLE THE TWO-REPEAT DESIGN H12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: H12; 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 8FJG 1 JRNL REVDAT 3 11-OCT-23 8FJG 1 JRNL REVDAT 2 04-OCT-23 8FJG 1 TITLE JRNL REVDAT 1 27-SEP-23 8FJG 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. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 11009 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 572 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 25.4900 - 3.3900 1.00 2643 152 0.2184 0.2500 REMARK 3 2 3.3900 - 2.6900 1.00 2692 132 0.3454 0.3284 REMARK 3 3 2.6900 - 2.3500 1.00 2633 144 0.2683 0.3779 REMARK 3 4 2.3500 - 2.1300 0.93 2469 144 0.3850 0.3903 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) : 0.347 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.782 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.98 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 : 0.008 889 REMARK 3 ANGLE : 0.904 1175 REMARK 3 CHIRALITY : 0.051 124 REMARK 3 PLANARITY : 0.004 147 REMARK 3 DIHEDRAL : 15.357 372 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 8FJG 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_1000270902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-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) : 0.98197 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 : 11009 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 REMARK 200 RESOLUTION RANGE LOW (A) : 25.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.920 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 (%): 39.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09 M SODIUM FLUORIDE, 0.09 M SODIUM REMARK 280 BROMIDE, 0.09 SODIUM IODIDE, 0.0499 M HEPES, 0.0501 M MOPS (ACID) REMARK 280 , 12.5% V/V MPD, 12.5% PEG 1000, AND 12.5% W/V PEG 3350, VAPOR REMARK 280 DIFFUSION, 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 15.22800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.72900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.29750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.72900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.22800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.29750 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 GLY A 105 REMARK 465 SER A 106 REMARK 465 GLY A 107 DBREF 8FJG A -1 107 PDB 8FJG 8FJG -1 107 SEQRES 1 A 109 SER GLY ASP ILE GLU LYS TYR PHE GLU GLU ALA LYS LYS SEQRES 2 A 109 LYS ILE ASP GLU GLU PHE GLU LYS LEU GLN THR ASP PRO SEQRES 3 A 109 SER VAL THR LEU GLU GLU PHE LYS GLU LYS LEU LYS LYS SEQRES 4 A 109 ILE LEU GLU GLU ALA TYR GLU LYS LEU LYS GLU ALA GLY SEQRES 5 A 109 TYR LYS GLY ILE GLU LYS TYR PHE GLU LYS MET GLU GLU SEQRES 6 A 109 LYS ILE LYS GLU GLU PHE GLU LYS LEU LYS LYS ASP PRO SEQRES 7 A 109 SER VAL THR LEU GLU ASP PHE LYS LYS LYS LEU LYS GLU SEQRES 8 A 109 ILE LEU ASP GLU MET LEU GLU ALA ILE LYS LYS SER GLY SEQRES 9 A 109 ILE SER GLY SER GLY FORMUL 2 HOH *5(H2 O) HELIX 1 AA1 ASP A 1 ASP A 23 1 23 HELIX 2 AA2 THR A 27 ALA A 49 1 23 HELIX 3 AA3 ILE A 54 ASP A 75 1 22 HELIX 4 AA4 THR A 79 SER A 101 1 23 CRYST1 30.456 46.595 73.458 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 0.032834 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013613 0.00000