HEADER DE NOVO PROTEIN 24-MAR-20 7BQD TITLE SOLUTION NMR STRUCTURE OF NF8 (KNOT FOLD); DE NOVO DESIGNED PROTEIN TITLE 2 WITH A NOVEL FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NF8; 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 7BQD 1 REMARK REVDAT 3 05-JUL-23 7BQD 1 JRNL REVDAT 2 14-JUN-23 7BQD 1 REMARK REVDAT 1 24-MAR-21 7BQD 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 7BQD 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_1300016038. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 56.5 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.95 MM [U-100% 13C; U-100% 15N] REMARK 210 NF8, 4.3 MM SODIUM PHOSPHATE, REMARK 210 5.7 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] NF8, 4.3 MM SODIUM REMARK 210 PHOSPHATE, 5.7 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 10 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, MAGRO 2.01.38, REMARK 210 NMRPIPE 2017, NMRVIEW 9.0, CYANA REMARK 210 3.98, TALOS 2017 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 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 13 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 15 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 20 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES 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 ASN A 31 45.19 -91.32 REMARK 500 1 LYS A 69 40.35 -77.50 REMARK 500 2 LYS A 69 30.73 -74.02 REMARK 500 3 ASN A 31 74.31 -100.90 REMARK 500 3 LYS A 69 24.30 -75.75 REMARK 500 3 HIS A 83 -33.72 -144.90 REMARK 500 3 HIS A 86 71.59 52.57 REMARK 500 4 HIS A 84 167.32 57.24 REMARK 500 5 HIS A 84 21.17 -143.13 REMARK 500 5 HIS A 86 -1.36 59.50 REMARK 500 6 ASN A 10 -11.13 -142.83 REMARK 500 6 LYS A 11 -51.03 64.02 REMARK 500 6 ASN A 31 48.70 -103.74 REMARK 500 6 HIS A 85 174.25 58.83 REMARK 500 7 ASN A 31 43.45 -83.96 REMARK 500 7 LYS A 69 40.78 -75.88 REMARK 500 7 HIS A 83 10.29 57.94 REMARK 500 7 HIS A 86 -171.43 55.24 REMARK 500 8 ASN A 31 53.76 -90.45 REMARK 500 9 ASN A 31 44.32 -93.31 REMARK 500 9 HIS A 83 -46.04 -146.19 REMARK 500 10 ASN A 31 49.17 -86.35 REMARK 500 10 LYS A 69 39.85 -79.71 REMARK 500 11 GLU A 12 -44.20 64.92 REMARK 500 11 ASN A 31 49.01 -81.02 REMARK 500 11 LYS A 69 35.52 -71.98 REMARK 500 12 LYS A 69 43.95 -80.30 REMARK 500 12 HIS A 83 -50.01 -148.92 REMARK 500 12 HIS A 86 166.20 60.79 REMARK 500 13 ASN A 31 55.88 -116.46 REMARK 500 13 LYS A 69 47.19 -72.30 REMARK 500 14 LYS A 69 31.01 -73.86 REMARK 500 14 HIS A 85 32.15 -97.64 REMARK 500 15 ASN A 31 48.63 -76.14 REMARK 500 15 HIS A 86 175.45 59.59 REMARK 500 16 LYS A 69 35.15 -80.90 REMARK 500 18 ASN A 31 55.88 -113.82 REMARK 500 18 LYS A 69 52.77 -115.87 REMARK 500 19 LYS A 69 46.43 -97.14 REMARK 500 20 ASN A 31 57.96 -96.69 REMARK 500 20 LYS A 69 33.29 -74.98 REMARK 500 20 HIS A 83 45.16 -149.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36333 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF NF8 (KNOT FOLD), DE NOVO DESIGNED PROTEIN REMARK 900 WITH A NOVEL FOLD DBREF 7BQD A 1 88 PDB 7BQD 7BQD 1 88 SEQRES 1 A 88 GLY THR ILE LEU ILE PHE LEU ASP LYS ASN LYS GLU GLN SEQRES 2 A 88 ALA GLU LYS LEU ALA LYS GLU VAL GLY VAL THR GLU ILE SEQRES 3 A 88 TYR GLU SER ASP ASN LEU GLU GLU LEU TYR ARG GLU ILE SEQRES 4 A 88 LYS GLU ARG ILE GLU ARG GLU ASN PRO ASN ALA THR ILE SEQRES 5 A 88 LEU THR VAL THR ASP PRO ASN GLU LEU LYS LYS ILE GLN SEQRES 6 A 88 ASP GLU GLY LYS VAL ASP ARG ILE ILE LEU LEU ILE LYS SEQRES 7 A 88 GLY SER LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASN A 10 GLY A 22 1 13 HELIX 2 AA2 ASN A 31 ASN A 47 1 17 HELIX 3 AA3 ASP A 57 GLY A 68 1 12 SHEET 1 AA1 4 ILE A 26 SER A 29 0 SHEET 2 AA1 4 ARG A 72 LYS A 78 1 O LEU A 75 N TYR A 27 SHEET 3 AA1 4 THR A 2 ASP A 8 1 N PHE A 6 O LEU A 76 SHEET 4 AA1 4 THR A 51 VAL A 55 1 O THR A 51 N ILE A 3 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