HEADER DE NOVO PROTEIN 25-MAR-20 7BQR TITLE SOLUTION NMR STRUCTURE OF FOLD-K MUSSOC; DE NOVO DESIGNED PROTEIN WITH TITLE 2 AN ASYMMETRIC ALL-ALPHA TOPOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUSSOC; 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,K.SAKUMA,T.KOSUGI,R.KOGA,N.KOGA REVDAT 4 15-MAY-24 7BQR 1 REMARK REVDAT 3 10-JAN-24 7BQR 1 JRNL REVDAT 2 14-JUN-23 7BQR 1 REMARK REVDAT 1 07-APR-21 7BQR 0 JRNL AUTH K.SAKUMA,N.KOBAYASHI,T.SUGIKI,T.NAGASHIMA,T.FUJIWARA, JRNL AUTH 2 K.SUZUKI,N.KOBAYASHI,T.MURATA,T.KOSUGI,R.KOGA,N.KOGA JRNL TITL DESIGN OF COMPLICATED ALL-ALPHA PROTEIN STRUCTURES JRNL REF NAT.STRUCT.MOL.BIOL. 2024 JRNL REFN ESSN 1545-9985 JRNL DOI 10.1038/S41594-023-01147-9 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 7BQR 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_1300016047. 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 : 160 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 FOLDK4, 1.06 MM POTASSIUM REMARK 210 PHOSPHATE, 2.97 MM SODIUM REMARK 210 PHOSPHATE, 155.2 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O; 0.2 MM REMARK 210 [U-100% 13C; U-100% 15N] FOLDK4, REMARK 210 1.06 MM POTASSIUM PHOSPHATE, REMARK 210 2.97 MM SODIUM PHOSPHATE, 155.2 REMARK 210 MM SODIUM CHLORIDE, 10.0 MG/ML REMARK 210 PF1 PHAGE, 95% 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 HCACO; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D C(CO) REMARK 210 NH; 3D H(CCO)NH; 3D H(NCA)NH; 3D REMARK 210 HCCH-TOCSY ALIPHATIC; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 2D 1H- REMARK 210 15N HSQC IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 900 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, QMDD REMARK 210 2.6, MAGRO 2.01.34, CYANA 3.98, REMARK 210 NMRVIEW 9.0, 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 10 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 5 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 10 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 12 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 89 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 13 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 83 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 ASP A 4 35.82 -76.49 REMARK 500 1 LYS A 124 -59.91 61.85 REMARK 500 2 LYS A 127 -71.22 61.03 REMARK 500 2 LEU A 130 -4.90 -140.08 REMARK 500 2 HIS A 132 -142.55 53.10 REMARK 500 2 HIS A 135 166.44 63.00 REMARK 500 3 GLU A 126 34.03 -78.92 REMARK 500 3 SER A 129 177.20 59.29 REMARK 500 3 GLU A 131 -16.51 58.05 REMARK 500 3 HIS A 136 46.51 -93.08 REMARK 500 4 LYS A 5 -45.69 61.55 REMARK 500 4 LYS A 125 -46.15 64.45 REMARK 500 4 LYS A 127 -31.48 -142.50 REMARK 500 5 GLU A 3 -45.48 -152.73 REMARK 500 6 ASP A 2 -42.45 64.67 REMARK 500 6 SER A 129 -12.52 -153.96 REMARK 500 7 LYS A 124 -169.18 57.42 REMARK 500 7 LEU A 130 -39.53 -136.77 REMARK 500 7 GLU A 131 -59.83 -160.07 REMARK 500 7 HIS A 132 8.08 55.98 REMARK 500 7 HIS A 136 177.54 55.51 REMARK 500 8 LYS A 127 147.74 63.75 REMARK 500 8 GLU A 131 154.51 63.66 REMARK 500 8 HIS A 133 161.98 62.58 REMARK 500 9 ASP A 4 160.49 63.67 REMARK 500 10 LYS A 125 -83.31 -140.88 REMARK 500 11 HIS A 136 165.07 60.55 REMARK 500 12 ASP A 4 -37.60 -139.27 REMARK 500 12 HIS A 136 -48.20 -147.79 REMARK 500 13 LYS A 124 -80.38 52.66 REMARK 500 13 GLU A 126 138.02 62.49 REMARK 500 14 SER A 129 178.03 61.36 REMARK 500 14 GLU A 131 165.61 59.47 REMARK 500 14 HIS A 135 169.20 63.00 REMARK 500 14 HIS A 136 179.91 59.11 REMARK 500 15 ASP A 2 -8.91 -141.38 REMARK 500 15 LYS A 125 127.68 56.75 REMARK 500 15 HIS A 135 -50.45 -134.33 REMARK 500 16 HIS A 135 172.61 59.86 REMARK 500 17 LYS A 125 42.80 -82.61 REMARK 500 18 GLU A 126 176.67 64.40 REMARK 500 18 LEU A 130 -124.23 49.22 REMARK 500 19 ASP A 4 -79.61 52.79 REMARK 500 19 LYS A 5 -38.73 59.28 REMARK 500 19 LYS A 127 -43.98 62.25 REMARK 500 19 SER A 129 -177.43 59.32 REMARK 500 20 LYS A 5 -38.87 60.41 REMARK 500 20 HIS A 132 17.27 55.01 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 13 ARG A 36 0.11 SIDE CHAIN REMARK 500 20 ARG A 87 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36338 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF FOLD-K MUSSOC; DE NOVO DESIGNED PROTEIN REMARK 900 WITH AN ASYMMETRIC ALL-ALPHA TOPOLOGY DBREF 7BQR A 1 137 PDB 7BQR 7BQR 1 137 SEQRES 1 A 137 GLY ASP GLU ASP LYS GLU LYS LEU LYS ARG GLU ALA GLU SEQRES 2 A 137 ARG ALA LEU SER GLU ALA LEU SER GLU PHE GLU LYS GLN SEQRES 3 A 137 GLY LYS ILE THR PRO GLU THR LEU LYS ARG LEU ALA GLU SEQRES 4 A 137 GLU ILE ALA GLU ALA ALA LEU ALA GLN GLN GLN GLY ASP SEQRES 5 A 137 SER GLU ARG LEU GLU LYS ALA ALA ARG ARG PHE ALA GLU SEQRES 6 A 137 THR LEU LEU ARG ALA LEU LYS GLU SER GLY ALA SER ALA SEQRES 7 A 137 GLU GLU ILE GLU GLU ALA ILE GLU ARG ILE ARG LYS ALA SEQRES 8 A 137 LEU SER LYS ALA PRO SER PRO GLN LEU GLN LYS LEU ALA SEQRES 9 A 137 ASN SER PRO GLN TRP GLN THR ALA LEU GLN GLU ALA ILE SEQRES 10 A 137 LYS LYS ALA ARG GLN GLU LYS LYS GLU LYS GLY SER LEU SEQRES 11 A 137 GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 LYS A 5 LEU A 20 1 16 HELIX 2 AA2 LEU A 20 GLN A 26 1 7 HELIX 3 AA3 THR A 30 GLY A 51 1 22 HELIX 4 AA4 ASP A 52 GLU A 73 1 22 HELIX 5 AA5 SER A 77 LYS A 94 1 18 HELIX 6 AA6 SER A 97 ASN A 105 1 9 HELIX 7 AA7 SER A 106 LYS A 124 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 2197 HIS A 137 ENDMDL MODEL 2 TER 2197 HIS A 137 ENDMDL MODEL 3 TER 2197 HIS A 137 ENDMDL MODEL 4 TER 2197 HIS A 137 ENDMDL MODEL 5 TER 2197 HIS A 137 ENDMDL MODEL 6 TER 2197 HIS A 137 ENDMDL MODEL 7 TER 2197 HIS A 137 ENDMDL MODEL 8 TER 2197 HIS A 137 ENDMDL MODEL 9 TER 2197 HIS A 137 ENDMDL MODEL 10 TER 2197 HIS A 137 ENDMDL MODEL 11 TER 2197 HIS A 137 ENDMDL MODEL 12 TER 2197 HIS A 137 ENDMDL MODEL 13 TER 2197 HIS A 137 ENDMDL MODEL 14 TER 2197 HIS A 137 ENDMDL MODEL 15 TER 2197 HIS A 137 ENDMDL MODEL 16 TER 2197 HIS A 137 ENDMDL MODEL 17 TER 2197 HIS A 137 ENDMDL MODEL 18 TER 2197 HIS A 137 ENDMDL MODEL 19 TER 2197 HIS A 137 ENDMDL MODEL 20 TER 2197 HIS A 137 ENDMDL MASTER 240 0 0 7 0 0 0 6 1092 1 0 11 END