HEADER DE NOVO PROTEIN 08-APR-24 9EXK TITLE SCALABLE PROTEIN DESIGN USING HALLUCINATION IN A RELAXED SEQUENCE TITLE 2 SPACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED PROTEIN K12; 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 DESIGNED PROTEIN K12, DE NOVO PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR C.J.FRANK,H.DIETZ REVDAT 1 16-OCT-24 9EXK 0 JRNL AUTH C.J.FRANK,H.DIETZ JRNL TITL EFFICIENT AND SCALABLE PROTEIN DESIGN USING A RELAXED JRNL TITL 2 SEQUENCE SPACE JRNL REF SCIENCE 2024 JRNL REFN ESSN 1095-9203 JRNL DOI 10.1126/SCIENCE.ADQ1741 REMARK 2 REMARK 2 RESOLUTION. 3.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.360 REMARK 3 NUMBER OF PARTICLES : 451357 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9EXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-24. REMARK 100 THE DEPOSITION ID IS D_1292137778. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : DE NOVO DESIGNED PROTEIN K12 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.60 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 100.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3740.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 120000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 50420 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 MET A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 GLY A 1001 REMARK 465 GLY A 1002 REMARK 465 SER A 1003 REMARK 465 HIS A 1004 REMARK 465 HIS A 1005 REMARK 465 HIS A 1006 REMARK 465 HIS A 1007 REMARK 465 HIS A 1008 REMARK 465 HIS A 1009 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 ASP A 129 -0.08 68.95 REMARK 500 ASN A 581 31.60 -97.03 REMARK 500 ASP A 676 53.06 -90.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50040 RELATED DB: EMDB REMARK 900 SCALABLE PROTEIN DESIGN USING HALLUCINATION IN A RELAXED SEQUENCE REMARK 900 SPACE DBREF 9EXK A -2 1009 PDB 9EXK 9EXK -2 1009 SEQRES 1 A 1012 MET SER GLY ALA VAL TYR PHE LEU LEU LEU ASP LEU ARG SEQRES 2 A 1012 ALA GLU VAL ASP GLU GLU ILE ALA TRP ALA ARG ARG LEU SEQRES 3 A 1012 GLY LEU ASP ASP LEU VAL ALA ALA LEU GLU ALA VAL ARG SEQRES 4 A 1012 ALA LEU ILE GLU GLY ALA LEU ALA THR LEU GLU SER ALA SEQRES 5 A 1012 ASP PHE ASP TYR LEU GLU PHE THR GLN ARG LEU ALA ASP SEQRES 6 A 1012 ALA LEU SER SER LEU VAL ARG VAL TYR ASP ASP LEU ILE SEQRES 7 A 1012 ALA ARG LEU GLU GLU GLN PRO ALA THR THR LEU ARG ARG SEQRES 8 A 1012 ALA TYR ARG ILE LEU LEU GLU TYR ARG ARG LYS GLU VAL SEQRES 9 A 1012 ARG GLU LEU LEU GLU ALA VAL GLN GLU LEU ARG ASP VAL SEQRES 10 A 1012 LEU GLU THR LEU GLU ARG LEU SER ARG ARG LEU GLY ARG SEQRES 11 A 1012 PRO ASP PHE ALA GLY TRP LEU VAL SER PHE VAL LEU ASP SEQRES 12 A 1012 HIS TYR GLY GLU LEU VAL ALA PRO ASP ILE LEU THR ASN SEQRES 13 A 1012 PRO ALA LYS GLY PHE ARG ALA LEU ALA HIS LEU LEU ARG SEQRES 14 A 1012 ALA PHE LEU TYR VAL LEU LEU ALA LEU LYS LEU ARG SER SEQRES 15 A 1012 PRO ASP GLU GLU LEU ARG GLU GLU ALA ARG ARG ALA VAL SEQRES 16 A 1012 ALA PHE LEU TYR GLY GLU GLU PHE VAL LYS ALA HIS SER SEQRES 17 A 1012 ASP GLU GLU LEU ALA GLU LEU LEU LEU GLU ARG ALA ARG SEQRES 18 A 1012 GLU ALA ILE LEU GLU ALA ALA ARG TYR ASN SER ALA LEU SEQRES 19 A 1012 ARG GLU GLU PHE ASP ALA ALA GLY GLY PRO GLU GLY ARG SEQRES 20 A 1012 GLU ALA TRP LEU GLU ARG GLN LEU LEU ARG LEU ARG GLY SEQRES 21 A 1012 LEU VAL GLU ARG PHE LEU GLU LEU TRP GLU ASN SER GLU SEQRES 22 A 1012 LEU ARG ALA GLY PRO ASP GLY GLU LEU VAL ALA VAL PRO SEQRES 23 A 1012 GLY VAL LYS GLY LEU GLU ILE ILE LYS LYS LEU LEU GLU SEQRES 24 A 1012 GLU GLY LYS GLY VAL ASN LEU ALA LEU TRP THR LEU GLY SEQRES 25 A 1012 ARG LEU LEU ARG ALA LEU ASP LEU SER PRO GLU ALA ARG SEQRES 26 A 1012 ALA ALA TYR GLU ALA ALA LEU GLU ALA LEU ARG ARG ALA SEQRES 27 A 1012 ARG LEU GLN LEU GLN TYR VAL GLN SER GLU ARG TYR GLU SEQRES 28 A 1012 GLY SER ASP ARG GLU ARG ALA GLU ALA ILE ARG ALA ALA SEQRES 29 A 1012 PHE GLU THR ILE ARG ALA ALA ALA GLU THR ILE ARG ALA SEQRES 30 A 1012 VAL ILE GLU ALA ASP THR SER LEU PRO ALA GLU LEU LYS SEQRES 31 A 1012 ALA ALA TYR ILE GLU VAL ILE TYR ALA TYR LEU LEU GLN SEQRES 32 A 1012 VAL ALA ARG GLU VAL ARG ASP ALA LEU TRP ARG LEU ALA SEQRES 33 A 1012 GLU GLU ILE LEU PRO GLU TYR ILE GLU LYS PHE PHE LYS SEQRES 34 A 1012 GLY SER GLU GLU GLU GLN ARG LEU THR LEU TYR GLU LEU SEQRES 35 A 1012 LEU ARG ALA LEU GLY GLU ASP TYR PHE PHE LEU ASP LEU SEQRES 36 A 1012 GLU LYS GLU GLY TYR SER GLU GLU GLU LEU ARG GLU LEU SEQRES 37 A 1012 PHE ARG ASN ALA LYS LEU GLU VAL ILE ASN ALA ASP GLU SEQRES 38 A 1012 SER GLY LYS ILE LYS LEU TYR ASN LEU ILE LEU ASP ALA SEQRES 39 A 1012 LYS LYS LEU ASN ARG LYS VAL LEU ILE LYS ILE THR LEU SEQRES 40 A 1012 THR GLU LEU SER GLU GLY SER TYR ILE ILE THR ILE GLU SEQRES 41 A 1012 VAL PHE LYS SER PRO ASP ALA GLU ILE PRO GLU TYR GLU SEQRES 42 A 1012 ILE ARG VAL ALA ALA VAL GLY ALA THR SER GLU GLU ILE SEQRES 43 A 1012 LEU LYS TYR LEU GLU GLU LEU LYS GLU LYS ALA LYS GLU SEQRES 44 A 1012 GLY GLU LEU ILE ARG GLU LEU LEU LEU LEU TYR VAL ASP SEQRES 45 A 1012 ARG GLN ILE ALA GLU LEU GLU GLU LYS VAL ALA ASN ALA SEQRES 46 A 1012 ASP LYS ILE ASP PRO VAL VAL ALA ARG LEU ALA ILE GLU SEQRES 47 A 1012 GLU ALA ARG ALA ARG GLY GLU GLU LEU THR GLU ALA ASP SEQRES 48 A 1012 VAL ILE GLU GLY THR ARG ALA GLY TYR GLN ALA ALA LEU SEQRES 49 A 1012 ASP VAL LEU ARG ARG ILE LYS ALA GLU LEU GLU LYS GLU SEQRES 50 A 1012 LYS SER PRO GLU ASN PRO PHE TYR GLN PHE TYR ASP LYS SEQRES 51 A 1012 LEU THR GLU LYS LEU LYS GLU LYS GLY PHE VAL SER GLU SEQRES 52 A 1012 GLU GLU ALA PHE GLU ILE ALA ARG GLU THR PHE GLY PHE SEQRES 53 A 1012 PRO ALA ASP LEU PRO PRO LEU ALA ALA ALA ALA LEU ARG SEQRES 54 A 1012 ASP PHE ALA SER THR VAL LEU THR ILE LEU GLU ILE PHE SEQRES 55 A 1012 LYS THR ALA GLU ASP PHE SER LYS TRP TYR LYS GLU ASN SEQRES 56 A 1012 LYS GLU LYS LEU ILE GLU LEU ALA GLY LEU SER GLU GLU SEQRES 57 A 1012 GLU LEU ASP LYS ILE VAL ARG LYS THR LEU THR LEU LEU SEQRES 58 A 1012 LEU GLU ALA LEU ALA ARG SER VAL PHE GLY SER LYS LEU SEQRES 59 A 1012 GLY ARG GLU LEU LEU ASN GLU ALA LEU GLY THR PHE ILE SEQRES 60 A 1012 LYS GLU LEU LEU GLU SER PHE PHE ARG THR HIS TYR GLY SEQRES 61 A 1012 LEU THR ARG GLY ASP ALA VAL ILE ASP PHE ASP ALA LYS SEQRES 62 A 1012 THR GLY ILE LEU SER LEU ARG PHE THR PRO ARG ALA TYR SEQRES 63 A 1012 ALA ARG ILE ARG VAL LYS GLU TYR ARG ASP PRO SER LEU SEQRES 64 A 1012 GLY GLU LYS PHE ASP ASN LEU LEU ASP VAL LEU SER SER SEQRES 65 A 1012 ASN PRO SER LEU LYS GLY GLN VAL ASP ARG LEU ARG VAL SEQRES 66 A 1012 SER TYR ALA PHE GLY THR PRO VAL GLY THR THR PRO ALA SEQRES 67 A 1012 LEU ARG ASP ALA THR ALA GLU ASP LEU GLU THR ASP PRO SEQRES 68 A 1012 ARG LEU LYS ARG HIS ARG ASP PHE ILE GLU GLU VAL GLU SEQRES 69 A 1012 ASN LEU TYR ALA GLU LEU LEU ILE ARG LEU GLU GLU ALA SEQRES 70 A 1012 LEU LYS ASP GLU PRO GLU THR VAL GLU ILE LEU THR GLU SEQRES 71 A 1012 ILE ILE GLY ARG HIS LEU LYS GLU VAL ILE HIS ASP PRO SEQRES 72 A 1012 ASP VAL ILE ASN ALA LEU LEU ASP ARG ARG ASP LEU SER SEQRES 73 A 1012 PRO GLU GLU PHE ALA ALA ARG ALA ARG ALA VAL LEU ASP SEQRES 74 A 1012 GLU ILE ILE ALA GLU GLU LYS LYS LEU GLN GLU LYS LEU SEQRES 75 A 1012 LEU GLU ALA VAL GLU ASP ASN PRO GLU ALA LYS LYS ILE SEQRES 76 A 1012 VAL GLU GLU ILE PHE PRO LYS ILE ILE ALA THR ILE GLU SEQRES 77 A 1012 ARG TYR ARG GLU TRP PRO GLU ARG GLU LEU ALA GLY LEU SEQRES 78 A 1012 PRO LEU GLY GLY SER HIS HIS HIS HIS HIS HIS HELIX 1 AA1 VAL A 2 GLY A 24 1 23 HELIX 2 AA2 LEU A 28 GLU A 47 1 20 HELIX 3 AA3 ASP A 52 GLN A 81 1 30 HELIX 4 AA4 THR A 84 GLY A 126 1 43 HELIX 5 AA5 ASP A 129 ASN A 153 1 25 HELIX 6 AA6 ASN A 153 ARG A 178 1 26 HELIX 7 AA7 ASP A 181 GLY A 197 1 17 HELIX 8 AA8 GLY A 197 LYS A 202 1 6 HELIX 9 AA9 SER A 205 ASN A 228 1 24 HELIX 10 AB1 ASN A 228 GLY A 239 1 12 HELIX 11 AB2 GLY A 240 GLU A 267 1 28 HELIX 12 AB3 GLY A 284 GLU A 296 1 13 HELIX 13 AB4 GLY A 300 ALA A 314 1 15 HELIX 14 AB5 SER A 318 GLN A 343 1 26 HELIX 15 AB6 SER A 350 ASP A 379 1 30 HELIX 16 AB7 PRO A 383 LEU A 412 1 30 HELIX 17 AB8 LEU A 412 LYS A 426 1 15 HELIX 18 AB9 SER A 428 GLY A 444 1 17 HELIX 19 AC1 GLU A 445 LYS A 454 1 10 HELIX 20 AC2 SER A 458 ASN A 468 1 11 HELIX 21 AC3 THR A 539 GLU A 556 1 18 HELIX 22 AC4 GLU A 558 ASN A 581 1 24 HELIX 23 AC5 ALA A 582 ILE A 585 5 4 HELIX 24 AC6 ASP A 586 ALA A 599 1 14 HELIX 25 AC7 THR A 605 LYS A 633 1 29 HELIX 26 AC8 ASN A 639 LYS A 655 1 17 HELIX 27 AC9 SER A 659 GLY A 672 1 14 HELIX 28 AD1 PRO A 678 GLY A 721 1 44 HELIX 29 AD2 SER A 723 SER A 745 1 23 HELIX 30 AD3 GLY A 748 GLY A 777 1 30 HELIX 31 AD4 THR A 799 ASP A 813 1 15 HELIX 32 AD5 PRO A 814 SER A 829 1 16 HELIX 33 AD6 LEU A 833 GLY A 847 1 15 HELIX 34 AD7 THR A 853 ARG A 857 5 5 HELIX 35 AD8 GLU A 862 THR A 866 5 5 HELIX 36 AD9 ASP A 867 LEU A 895 1 29 HELIX 37 AE1 GLU A 898 ILE A 917 1 20 HELIX 38 AE2 ASP A 919 ASP A 928 1 10 HELIX 39 AE3 SER A 933 VAL A 963 1 31 HELIX 40 AE4 ASN A 966 TRP A 990 1 25 HELIX 41 AE5 ARG A 993 GLY A 997 5 5 SHEET 1 AA1 2 GLU A 270 ALA A 273 0 SHEET 2 AA1 2 LEU A 279 VAL A 282 -1 O VAL A 280 N ARG A 272 SHEET 1 AA2 5 LYS A 470 ASN A 475 0 SHEET 2 AA2 5 ILE A 482 ALA A 491 -1 O LEU A 484 N ILE A 474 SHEET 3 AA2 5 ARG A 496 SER A 508 -1 O VAL A 498 N LEU A 489 SHEET 4 AA2 5 SER A 511 PHE A 519 -1 O PHE A 519 N LEU A 499 SHEET 5 AA2 5 ILE A 531 VAL A 536 -1 O VAL A 536 N TYR A 512 SHEET 1 AA3 2 ALA A 783 VAL A 784 0 SHEET 2 AA3 2 ARG A 797 PHE A 798 -1 O ARG A 797 N VAL A 784 SHEET 1 AA4 2 PHE A 787 ASP A 788 0 SHEET 2 AA4 2 ILE A 793 LEU A 794 -1 O ILE A 793 N ASP A 788 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000