HEADER DE NOVO PROTEIN 24-MAR-20 7BQC TITLE SOLUTION NMR STRUCTURE OF NF4; DE NOVO DESIGNED PROTEIN WITH A NOVEL TITLE 2 FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NF4; 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.NAGASHIMA,S.MINAMI,R.KOGA,T.CHIKENJI,N.KOGA REVDAT 4 15-MAY-24 7BQC 1 REMARK REVDAT 3 05-JUL-23 7BQC 1 JRNL REVDAT 2 14-JUN-23 7BQC 1 REMARK REVDAT 1 24-MAR-21 7BQC 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 7BQC 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_1300016036. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 145.5 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.45 MM [U-100% 13C; U-100% 15N] REMARK 210 NF4, 5.6 MM SODIUM PHOSPHATE, REMARK 210 1.1 MM POTASSIUM PHOSPHATE, 137 REMARK 210 MM SODIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 0.2 MM [U-100% 13C; U-100% REMARK 210 15N] NF4, 5.6 MM SODIUM REMARK 210 PHOSPHATE, 1.1 MM POTASSIUM REMARK 210 PHOSPHATE, 137 MM SODIUM REMARK 210 CHLORIDE, 10 MG/ML PF1 PHAGE, 95% REMARK 210 H2O/5% 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 HNCO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY REMARK 210 ALIPHATIC; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D 1H-15N REMARK 210 HSQC IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 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, CYANA 3.98, REMARK 210 TALOS 2017, QMDD 2.6 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 2 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 10 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 6 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 14 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 15 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 16 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 19 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 20 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.4 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 GLU A 74 -22.67 58.81 REMARK 500 1 GLU A 119 -169.97 57.75 REMARK 500 1 HIS A 123 135.20 61.27 REMARK 500 2 GLU A 74 39.88 -85.87 REMARK 500 2 ASN A 90 45.11 -99.86 REMARK 500 2 HIS A 124 -177.17 57.27 REMARK 500 3 GLU A 74 -40.85 59.74 REMARK 500 3 SER A 115 37.03 -77.79 REMARK 500 3 TRP A 116 -54.03 -131.33 REMARK 500 3 HIS A 120 17.43 58.06 REMARK 500 4 GLU A 74 -31.02 62.77 REMARK 500 4 SER A 117 -48.94 -151.46 REMARK 500 4 LEU A 118 150.21 63.18 REMARK 500 4 HIS A 120 34.54 -79.43 REMARK 500 5 PRO A 21 -172.10 -69.66 REMARK 500 5 ASN A 22 -42.72 68.07 REMARK 500 5 ASN A 72 -46.56 -162.63 REMARK 500 6 ASN A 72 -31.61 60.36 REMARK 500 6 SER A 115 -170.20 59.73 REMARK 500 6 GLU A 119 34.99 -86.55 REMARK 500 7 GLU A 74 -32.76 60.11 REMARK 500 8 GLU A 74 -39.20 61.15 REMARK 500 8 HIS A 121 37.81 -146.11 REMARK 500 8 HIS A 122 155.73 63.37 REMARK 500 9 ASN A 72 -85.78 42.62 REMARK 500 9 GLU A 74 31.93 -80.30 REMARK 500 9 ASN A 90 16.64 57.91 REMARK 500 9 HIS A 124 -35.08 58.94 REMARK 500 10 ASN A 72 -1.12 64.33 REMARK 500 11 ASN A 72 -32.73 -162.68 REMARK 500 11 SER A 117 -176.55 57.20 REMARK 500 11 HIS A 121 -49.76 -149.53 REMARK 500 12 GLU A 74 -20.61 55.86 REMARK 500 12 HIS A 124 -51.34 -152.16 REMARK 500 13 PRO A 21 -178.53 -69.51 REMARK 500 13 ASN A 22 -40.61 68.66 REMARK 500 13 GLU A 74 -23.74 61.19 REMARK 500 13 HIS A 123 -154.95 56.38 REMARK 500 14 GLU A 74 -34.20 64.28 REMARK 500 14 ASN A 90 13.25 58.62 REMARK 500 15 GLU A 74 -28.94 61.09 REMARK 500 15 ASN A 90 19.13 59.67 REMARK 500 15 TRP A 116 -169.79 56.48 REMARK 500 15 SER A 117 -161.29 57.68 REMARK 500 15 LEU A 118 -76.95 -111.47 REMARK 500 16 ASN A 72 124.06 59.20 REMARK 500 16 LEU A 118 -48.08 -155.75 REMARK 500 17 GLU A 74 -15.52 56.32 REMARK 500 17 HIS A 123 157.17 62.70 REMARK 500 18 ARG A 71 -149.35 -82.38 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. 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 2 ARG A 97 0.09 SIDE CHAIN REMARK 500 5 ARG A 97 0.08 SIDE CHAIN REMARK 500 10 ARG A 79 0.10 SIDE CHAIN REMARK 500 11 ARG A 79 0.08 SIDE CHAIN REMARK 500 16 ARG A 79 0.08 SIDE CHAIN REMARK 500 18 ARG A 79 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36332 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF NF4, DE NOVO DESIGNED PROTEIN WITH A REMARK 900 NOVEL FOLD DBREF 7BQC A 1 125 PDB 7BQC 7BQC 1 125 SEQRES 1 A 125 GLY SER GLU GLU ILE ARG GLU LEU VAL ARG LYS ILE TYR SEQRES 2 A 125 GLU THR VAL ARG LYS GLU ASN PRO ASN VAL LYS ILE LEU SEQRES 3 A 125 ILE PHE ILE ILE PHE THR SER ASP GLY THR ILE LYS VAL SEQRES 4 A 125 ILE ILE VAL ILE ILE ALA ASP ASP PRO ASN ASP ALA LYS SEQRES 5 A 125 ARG ILE VAL LYS LYS ILE GLN GLU ARG PHE PRO LYS LEU SEQRES 6 A 125 THR ILE LYS GLN SER ARG ASN GLU GLU GLU ALA GLU LYS SEQRES 7 A 125 ARG ILE GLN LYS GLU LEU GLU GLU ARG ASN PRO ASN ALA SEQRES 8 A 125 GLU ILE GLN VAL VAL ARG SER GLU ASP GLU LEU LYS GLU SEQRES 9 A 125 ILE LEU ASP LYS LEU ASP GLU LYS LYS GLY SER TRP SER SEQRES 10 A 125 LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 GLY A 1 ASN A 20 1 20 HELIX 2 AA2 ASP A 47 PHE A 62 1 16 HELIX 3 AA3 GLU A 75 ASN A 88 1 14 HELIX 4 AA4 SER A 98 GLY A 114 1 17 SHEET 1 AA1 4 THR A 66 SER A 70 0 SHEET 2 AA1 4 ILE A 37 ILE A 44 1 N ILE A 41 O LYS A 68 SHEET 3 AA1 4 LYS A 24 THR A 32 -1 N PHE A 28 O ILE A 40 SHEET 4 AA1 4 ALA A 91 VAL A 96 -1 O VAL A 96 N ILE A 27 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