HEADER DE NOVO PROTEIN 24-MAR-20 7BQE TITLE SOLUTION NMR STRUCTURE OF NF3; DE NOVO DESIGNED PROTEIN WITH A NOVEL TITLE 2 FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NF3; 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, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.KOBAYASHI,T.SUGIKI,T.FUJIWARA,S.MINAMI,R.KOGA,G.CHIKENJI,N.KOGA REVDAT 4 15-MAY-24 7BQE 1 REMARK REVDAT 3 05-JUL-23 7BQE 1 JRNL REVDAT 2 14-JUN-23 7BQE 1 REMARK REVDAT 1 24-MAR-21 7BQE 0 JRNL AUTH S.MINAMI,N.KOBAYASHI,T.SUGIKI,T.NAGASHIMA,T.FUJIWARA,R.KOGA, JRNL AUTH 2 G.CHIKENJI,N.KOGA JRNL TITL EXPLORATION OF NOVEL ALPHA-BETA-PROTEIN FOLDS THROUGH DE JRNL TITL 2 NOVO DESIGN JRNL REF NAT.STRUCT.MOL.BIOL. 2023 JRNL REFN ESSN 1545-9985 JRNL DOI 10.1038/S41594-023-01029-0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7BQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016039. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 58.5 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-100% 13C; U-100% 15N] REMARK 210 NF3, 1.1 MM SODIUM PHOSPHATE, REMARK 210 7.4 MM POTASSIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 0.2 MM [U-100% 13C; U-100% REMARK 210 15N] NF3, 1.1 MM SODIUM REMARK 210 PHOSPHATE, 7.4 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 6 MG/ML PF1 PHAGE, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D BEST-HNCO; 3D BEST- REMARK 210 HNCACB; 3D BEST-HN(CO)CACB; 3D REMARK 210 HCCH-TOCSY ALIPHATIC; 3D HCCH- REMARK 210 TOCSY AROMATIC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D 1H-15N REMARK 210 HSQC IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.2, NMRPIPE 2017, MAGRO REMARK 210 2.01.38, NMRVIEW 9.0, TALOS 2017, REMARK 210 CYANA 3.98 REMARK 210 METHOD USED : MOLECULAR 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 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 10 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 10 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 13 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 13 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 60 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 SER A 100 47.36 -89.64 REMARK 500 2 SER A 100 46.13 -90.69 REMARK 500 2 SER A 102 -176.75 59.35 REMARK 500 2 HIS A 105 -119.15 -153.66 REMARK 500 3 TRP A 101 -85.62 53.72 REMARK 500 3 LEU A 103 49.56 -82.97 REMARK 500 3 HIS A 108 145.50 63.94 REMARK 500 5 TRP A 101 132.67 59.55 REMARK 500 5 SER A 102 172.65 61.55 REMARK 500 5 HIS A 105 -59.20 -150.19 REMARK 500 6 TRP A 101 -86.57 -128.39 REMARK 500 6 LEU A 103 15.52 -148.23 REMARK 500 6 HIS A 105 -36.13 59.55 REMARK 500 6 HIS A 108 79.91 54.57 REMARK 500 6 HIS A 109 167.21 63.16 REMARK 500 8 SER A 100 36.88 -95.94 REMARK 500 8 SER A 102 36.79 -88.65 REMARK 500 8 HIS A 106 -172.49 57.27 REMARK 500 8 HIS A 109 -64.28 -130.27 REMARK 500 9 TRP A 101 -103.52 46.56 REMARK 500 10 TRP A 101 -164.76 52.29 REMARK 500 10 HIS A 106 73.18 52.52 REMARK 500 10 HIS A 108 49.64 -81.74 REMARK 500 11 SER A 100 76.60 -111.32 REMARK 500 11 SER A 102 96.87 -60.40 REMARK 500 11 LEU A 103 17.79 -154.25 REMARK 500 11 HIS A 106 -89.19 36.77 REMARK 500 12 SER A 100 60.30 -105.14 REMARK 500 12 SER A 102 42.89 -77.71 REMARK 500 12 HIS A 108 106.58 57.69 REMARK 500 12 HIS A 109 179.10 59.66 REMARK 500 13 ASN A 75 82.86 -150.13 REMARK 500 13 SER A 102 176.71 57.76 REMARK 500 13 HIS A 106 38.50 -140.27 REMARK 500 15 SER A 100 46.36 -92.44 REMARK 500 15 HIS A 105 2.87 54.99 REMARK 500 15 HIS A 107 -33.87 -145.58 REMARK 500 16 SER A 100 45.71 -88.70 REMARK 500 17 LEU A 103 34.94 -83.78 REMARK 500 17 HIS A 105 -168.04 55.37 REMARK 500 17 HIS A 108 -152.12 51.85 REMARK 500 19 SER A 102 156.07 62.25 REMARK 500 19 LEU A 103 25.47 -141.98 REMARK 500 19 HIS A 108 -41.22 -153.83 REMARK 500 20 SER A 102 120.86 -36.03 REMARK 500 20 LEU A 103 16.77 -151.21 REMARK 500 20 HIS A 108 -158.17 50.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 9 ARG A 44 0.08 SIDE CHAIN REMARK 500 19 ARG A 44 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36334 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF NF3, DE NOVO DESIGNED PROTEIN WITH A REMARK 900 NOVEL FOLD DBREF 7BQE A 1 110 PDB 7BQE 7BQE 1 110 SEQRES 1 A 110 GLY SER ASP GLU GLU ILE ARG LYS LYS LEU GLU GLU LEU SEQRES 2 A 110 ALA LYS ARG LYS GLY LYS ASP LEU GLN LEU ARG ARG TYR SEQRES 3 A 110 ASN ASP PRO ASN GLU VAL GLU LYS SER ILE ARG GLU ALA SEQRES 4 A 110 LEU LYS LYS GLY ARG THR LEU ILE ILE ILE ILE ASN GLY SEQRES 5 A 110 VAL PHE VAL VAL VAL SER THR ASP GLU ASP LEU ILE ARG SEQRES 6 A 110 GLU ILE LYS ARG LEU ILE LYS GLU SER ASN PRO ASN LYS SEQRES 7 A 110 LYS THR LEU ASP VAL THR THR GLU GLU ASP LEU GLU GLU SEQRES 8 A 110 VAL LEU ARG ARG ILE LYS LYS GLY SER TRP SER LEU GLU SEQRES 9 A 110 HIS HIS HIS HIS HIS HIS HELIX 1 AA1 GLY A 1 GLY A 18 1 18 HELIX 2 AA2 ASP A 28 GLY A 43 1 16 HELIX 3 AA3 ASP A 60 ASN A 75 1 16 HELIX 4 AA4 THR A 85 GLY A 99 1 15 HELIX 5 AA5 HIS A 105 HIS A 110 1 6 SHEET 1 AA1 4 LEU A 21 TYR A 26 0 SHEET 2 AA1 4 THR A 45 ILE A 50 1 O ILE A 47 N GLN A 22 SHEET 3 AA1 4 VAL A 53 VAL A 57 -1 O VAL A 57 N LEU A 46 SHEET 4 AA1 4 THR A 80 VAL A 83 1 O LEU A 81 N VAL A 56 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