HEADER DE NOVO PROTEIN 19-DEC-24 9HSA TITLE SOLUTION STRUCTURE OF X55, A COMPUTATIONALLY DESIGNED PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: X55; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPUTATIONAL DESIGN, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.SCHWEIMER,J.HENNIG,C.PEREZ-BORRAJERO REVDAT 3 17-SEP-25 9HSA 1 JRNL REVDAT 2 02-JUL-25 9HSA 1 JRNL REVDAT 1 23-APR-25 9HSA 0 JRNL AUTH M.A.JENDRUSCH,A.L.J.YANG,E.CACACE,J.BOBONIS,C.G.P.VOOGDT, JRNL AUTH 2 S.KASPAR,K.SCHWEIMER,C.PEREZ-BORRAJERO,K.LAPOUGE, JRNL AUTH 3 J.SCHEURICH,K.REMANS,J.HENNIG,A.TYPAS,J.O.KORBEL,S.K.SADIQ JRNL TITL ALPHADESIGN: A DE NOVO PROTEIN DESIGN FRAMEWORK BASED ON JRNL TITL 2 ALPHAFOLD. JRNL REF MOL.SYST.BIOL. V. 21 1166 2025 JRNL REFN ESSN 1744-4292 JRNL PMID 40527958 JRNL DOI 10.1038/S44320-025-00119-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9HSA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292144143. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.36 MM [U-100% 15N] X55, 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 0.3 REMARK 210 MM [U-100% 13C; U-100% 15N] X55, REMARK 210 50 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HN(CO)CA; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 2D 1H-13C REMARK 210 HSQC ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 LYS A 4 77.63 59.11 REMARK 500 1 LYS A 12 94.62 57.71 REMARK 500 1 GLU A 15 160.51 63.05 REMARK 500 1 PRO A 16 92.80 -69.77 REMARK 500 1 LYS A 32 98.37 -179.98 REMARK 500 1 SER A 73 75.24 -112.71 REMARK 500 1 PRO A 74 78.17 -69.75 REMARK 500 1 LEU A 75 -39.05 -166.78 REMARK 500 1 VAL A 76 87.87 -67.16 REMARK 500 1 ASP A 98 102.53 -52.80 REMARK 500 1 PRO A 100 75.35 -69.70 REMARK 500 1 PHE A 101 -49.33 -154.93 REMARK 500 2 GLU A 5 51.11 -102.10 REMARK 500 2 LYS A 9 71.78 -116.34 REMARK 500 2 PRO A 11 -171.94 -69.78 REMARK 500 2 PRO A 14 -170.85 -69.79 REMARK 500 2 TRP A 17 79.08 52.12 REMARK 500 2 LYS A 32 92.02 -174.94 REMARK 500 2 SER A 73 75.86 -112.71 REMARK 500 2 PRO A 74 83.52 -69.80 REMARK 500 2 LEU A 75 -35.96 -175.95 REMARK 500 2 VAL A 76 87.19 -67.85 REMARK 500 2 ASP A 98 102.41 -52.90 REMARK 500 2 PRO A 100 75.69 -69.83 REMARK 500 2 PHE A 101 -61.01 -155.08 REMARK 500 3 MET A 2 -55.37 -148.09 REMARK 500 3 LYS A 4 45.84 -162.57 REMARK 500 3 GLU A 5 53.31 -156.30 REMARK 500 3 SER A 8 -56.89 -166.55 REMARK 500 3 GLU A 31 33.29 -93.21 REMARK 500 3 LYS A 32 32.54 -175.73 REMARK 500 3 SER A 73 77.91 -111.66 REMARK 500 3 PRO A 74 78.00 -69.73 REMARK 500 3 LEU A 75 -42.36 -163.68 REMARK 500 3 ASN A 96 60.74 67.35 REMARK 500 3 ASP A 98 103.23 -52.00 REMARK 500 3 PRO A 100 73.76 -69.79 REMARK 500 3 PHE A 101 -56.31 -154.88 REMARK 500 4 LYS A 4 -62.72 -126.11 REMARK 500 4 GLU A 5 98.36 60.59 REMARK 500 4 ILE A 7 149.03 64.93 REMARK 500 4 LYS A 12 -67.59 -175.28 REMARK 500 4 LYS A 32 100.13 179.97 REMARK 500 4 SER A 73 76.74 -112.25 REMARK 500 4 PRO A 74 77.86 -69.82 REMARK 500 4 LEU A 75 -40.80 -164.37 REMARK 500 4 VAL A 76 86.46 -68.44 REMARK 500 4 ASN A 96 63.79 67.31 REMARK 500 4 ASP A 98 108.07 -51.60 REMARK 500 4 PRO A 100 75.76 -69.73 REMARK 500 REMARK 500 THIS ENTRY HAS 266 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34973 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF X55, A COMPUTATIONALLY DESIGNED PROTEIN DBREF 9HSA A 1 102 PDB 9HSA 9HSA 1 102 SEQRES 1 A 102 SER MET ASP LYS GLU TRP ILE SER LYS LEU PRO LYS SER SEQRES 2 A 102 PRO GLU PRO TRP THR PRO GLU GLN GLU GLU ALA PHE LEU SEQRES 3 A 102 LYS ARG PHE ALA GLU LYS VAL ASP PRO GLU GLU THR LEU SEQRES 4 A 102 LYS LYS LEU GLU GLU TRP ILE LYS GLU ASN ILE LYS LYS SEQRES 5 A 102 TYR PRO GLU TYR LYS ASP GLU LEU GLU VAL ALA TYR ASN SEQRES 6 A 102 SER ALA LYS LEU PHE LEU GLU SER PRO LEU VAL GLU GLY SEQRES 7 A 102 PRO GLY LYS VAL ARG ALA ILE GLY ARG VAL LEU TRP THR SEQRES 8 A 102 ILE LYS ARG LEU ASN ILE ASP SER PRO PHE VAL HELIX 1 AA1 THR A 18 GLU A 31 1 14 HELIX 2 AA2 ASP A 34 TYR A 53 1 20 HELIX 3 AA3 TYR A 56 SER A 73 1 18 HELIX 4 AA4 GLY A 78 ASN A 96 1 19 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1 TER 1713 VAL A 102 ENDMDL MODEL 2 TER 1713 VAL A 102 ENDMDL MODEL 3 TER 1713 VAL A 102 ENDMDL MODEL 4 TER 1713 VAL A 102 ENDMDL MODEL 5 TER 1713 VAL A 102 ENDMDL MODEL 6 TER 1713 VAL A 102 ENDMDL MODEL 7 TER 1713 VAL A 102 ENDMDL MODEL 8 TER 1713 VAL A 102 ENDMDL MODEL 9 TER 1713 VAL A 102 ENDMDL MODEL 10 TER 1713 VAL A 102 ENDMDL MODEL 11 TER 1713 VAL A 102 ENDMDL MODEL 12 TER 1713 VAL A 102 ENDMDL MODEL 13 TER 1713 VAL A 102 ENDMDL MODEL 14 TER 1713 VAL A 102 ENDMDL MODEL 15 TER 1713 VAL A 102 ENDMDL MODEL 16 TER 1713 VAL A 102 ENDMDL MODEL 17 TER 1713 VAL A 102 ENDMDL MODEL 18 TER 1713 VAL A 102 ENDMDL MODEL 19 TER 1713 VAL A 102 ENDMDL MODEL 20 TER 1713 VAL A 102 ENDMDL MASTER 150 0 0 4 0 0 0 6 850 1 0 8 END