HEADER DE NOVO PROTEIN 11-JAN-24 8VL4 TITLE SOLUTION NMR STRUCTURE OF DE NOVO DESIGN PROTEIN 312 PARENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGN PROTEIN 312 PARENT; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DE NOVO DESIGN, MACHINE LEARNING, FOLD-SWITCHING, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.C.MCSHAN,M.K.SIMMA REVDAT 3 20-AUG-25 8VL4 1 JRNL REVDAT 2 04-DEC-24 8VL4 1 JRNL REVDAT 1 07-AUG-24 8VL4 0 JRNL AUTH S.L.LISANZA,J.M.GERSHON,S.W.K.TIPPS,J.N.SIMS,L.ARNOLDT, JRNL AUTH 2 S.J.HENDEL,M.K.SIMMA,G.LIU,M.YASE,H.WU,C.D.THARP,X.LI, JRNL AUTH 3 A.KANG,E.BRACKENBROUGH,A.K.BERA,S.GERBEN,B.J.WITTMANN, JRNL AUTH 4 A.C.MCSHAN,D.BAKER JRNL TITL MULTISTATE AND FUNCTIONAL PROTEIN DESIGN USING ROSETTAFOLD JRNL TITL 2 SEQUENCE SPACE DIFFUSION. JRNL REF NAT.BIOTECHNOL. V. 43 1288 2025 JRNL REFN ISSN 1087-0156 JRNL PMID 39322764 JRNL DOI 10.1038/S41587-024-02395-W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CS-ROSETTA REMARK 3 AUTHORS : SHEN, VERNON, BAKER AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8VL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000280462. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.15 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 205 UM [U-13C; U-15N] 312 REMARK 210 PARENT, 100MM NACL, 20MM SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC; 3D HNCA; 3D HNCACB; 3D REMARK 210 HNCO; 3D CBCA(CO)NH; 3D 1H-15N REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, TALOS-N, CS REMARK 210 -ROSETTA REMARK 210 METHOD USED : NA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 3000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 103 REMARK 465 SER A 104 REMARK 465 HIS A 105 REMARK 465 HIS A 106 REMARK 465 TRP A 107 REMARK 465 GLY A 108 REMARK 465 SER A 109 REMARK 465 HIS A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 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 TYR A 61 129.14 -171.17 REMARK 500 2 TYR A 61 128.88 -171.65 REMARK 500 4 TYR A 61 129.11 -172.13 REMARK 500 5 TYR A 61 128.93 -171.07 REMARK 500 6 VAL A 41 -68.28 -95.20 REMARK 500 7 TYR A 61 129.49 -171.76 REMARK 500 8 TYR A 61 131.96 -170.24 REMARK 500 10 TYR A 61 144.71 -179.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31137 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF DE NOVO DESIGN PROTEIN 312 PARENT DBREF 8VL4 A 1 115 PDB 8VL4 8VL4 1 115 SEQRES 1 A 115 GLY LEU LEU THR ARG GLU GLU ILE GLU ALA ALA LEU LYS SEQRES 2 A 115 GLU ALA GLY PHE THR GLU GLU GLU ILE ARG LYS VAL LEU SEQRES 3 A 115 ALA TRP LEU GLU ARG VAL GLY GLY GLU ARG LYS VAL LEU SEQRES 4 A 115 LYS VAL ALA GLY LYS ILE LEU ILE ILE VAL GLU LYS ARG SEQRES 5 A 115 ALA GLY SER ARG LEU LEU LEU LEU TYR ALA GLY ARG VAL SEQRES 6 A 115 ILE GLU LYS GLU GLY MET SER ARG GLU GLU VAL GLU ALA SEQRES 7 A 115 ILE LYS GLN LEU ILE SER ALA GLY ALA THR VAL GLU GLU SEQRES 8 A 115 ILE GLU ALA ILE ILE LYS ARG ILE GLU ALA ARG GLY SER SEQRES 9 A 115 HIS HIS TRP GLY SER HIS HIS HIS HIS HIS HIS HELIX 1 AA1 THR A 4 GLY A 16 1 13 HELIX 2 AA2 THR A 18 GLY A 33 1 16 HELIX 3 AA3 SER A 72 ALA A 85 1 14 HELIX 4 AA4 THR A 88 ALA A 101 1 14 SHEET 1 AA1 4 GLU A 35 VAL A 41 0 SHEET 2 AA1 4 LYS A 44 GLU A 50 -1 O LEU A 46 N LEU A 39 SHEET 3 AA1 4 SER A 55 TYR A 61 -1 O ARG A 56 N VAL A 49 SHEET 4 AA1 4 ARG A 64 MET A 71 -1 O MET A 71 N SER A 55 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 1667 ARG A 102 ENDMDL MODEL 2 TER 1667 ARG A 102 ENDMDL MODEL 3 TER 1667 ARG A 102 ENDMDL MODEL 4 TER 1667 ARG A 102 ENDMDL MODEL 5 TER 1667 ARG A 102 ENDMDL MODEL 6 TER 1667 ARG A 102 ENDMDL MODEL 7 TER 1667 ARG A 102 ENDMDL MODEL 8 TER 1667 ARG A 102 ENDMDL MODEL 9 TER 1667 ARG A 102 ENDMDL MODEL 10 TER 1667 ARG A 102 ENDMDL MASTER 120 0 0 4 4 0 0 6 799 1 0 9 END