HEADER DE NOVO PROTEIN 25-MAR-20 7BQS TITLE SOLUTION NMR STRUCTURE OF FOLD-U NOMUR; DE NOVO DESIGNED PROTEIN WITH TITLE 2 AN ASYMMETRIC ALL-ALPHA TOPOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NOMUR; 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 PROTEINS, 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 7BQS 1 REMARK REVDAT 3 10-JAN-24 7BQS 1 JRNL REVDAT 2 14-JUN-23 7BQS 1 REMARK REVDAT 1 07-APR-21 7BQS 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 7BQS 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_1300016048. 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 : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 FOLDU5, 1.06 MM POTASSIUM REMARK 210 PHOSPHATE, 2.97 MM SODIUM REMARK 210 PHOSPHATE, 155.2 MM SODIUM REMARK 210 CHLORIDE, 10 UM EDTA, 0.02 % REMARK 210 SODIUM AZIDE, 0.16 % W/W REMARK 210 PROTEASE INHIBITOR COMPLETE REMARK 210 COCKTAIL, 95% H2O/5% D2O; 0.4 MM REMARK 210 [U-100% 13C; U-100% 15N] FOLDU5, REMARK 210 1.06 MM POTASSIUM PHOSPHATE, REMARK 210 2.97 MM SODIUM PHOSPHATE, 155.2 REMARK 210 MM SODIUM CHLORIDE, 10 MM EDTA, REMARK 210 0.02 % SODIUM AZIDE, 0.16 % W/W REMARK 210 PROTEASE INHIBITOR COMPLETE REMARK 210 COCKTAIL, 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 HN(CA)CO; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 3D C(CO)NH; 3D REMARK 210 H(CCO)NH; 3D (H)N(CA)NH; 3D REMARK 210 H(NCA)NH; 3D HBHA(CO)NH; 3D REMARK 210 HNHAHB; 3D HCCH-TOCSY ALIPHATIC; REMARK 210 3D HCCH-TOCSY AROMATIC; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-15N HSQC IPAP; REMARK 210 3D J-HNCO; 3D J-HN(CO)CA 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 3.5, NMRPIPE 2017, QMDD REMARK 210 2.6, MAGRO 2.01.32, 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 104 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 92 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 4 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 5 ARG A 92 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 5 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 6 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 8 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 110 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 10 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.1 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 61 53.74 -99.67 REMARK 500 1 ALA A 98 172.09 63.29 REMARK 500 1 ARG A 112 -33.31 -152.64 REMARK 500 1 HIS A 119 -32.61 -147.77 REMARK 500 1 HIS A 121 -15.72 -145.32 REMARK 500 2 ASN A 61 53.40 -98.75 REMARK 500 2 ALA A 98 170.17 64.90 REMARK 500 2 ARG A 112 -48.45 -154.61 REMARK 500 2 HIS A 117 -48.99 -153.27 REMARK 500 2 HIS A 121 -36.96 -156.63 REMARK 500 3 ASN A 61 52.55 -101.19 REMARK 500 3 ALA A 98 -175.50 62.63 REMARK 500 3 ARG A 112 -157.32 47.92 REMARK 500 3 LEU A 115 -39.94 -155.40 REMARK 500 3 GLU A 116 30.45 -145.34 REMARK 500 4 THR A 3 72.26 46.49 REMARK 500 4 ASN A 61 53.54 -100.55 REMARK 500 4 ALA A 98 174.89 66.17 REMARK 500 4 ARG A 112 -87.97 49.72 REMARK 500 4 SER A 114 94.58 50.11 REMARK 500 4 HIS A 119 -48.24 -155.69 REMARK 500 4 HIS A 120 179.12 59.20 REMARK 500 5 ASN A 61 52.89 -97.06 REMARK 500 5 ALA A 98 161.33 66.88 REMARK 500 5 HIS A 117 6.48 -153.52 REMARK 500 5 HIS A 119 -14.57 58.56 REMARK 500 5 HIS A 121 -178.77 58.05 REMARK 500 6 ASN A 61 54.75 -97.57 REMARK 500 6 ALA A 98 -177.97 -176.93 REMARK 500 6 GLU A 116 -57.61 -153.48 REMARK 500 6 HIS A 117 -45.61 -153.48 REMARK 500 6 HIS A 119 142.31 61.95 REMARK 500 7 ASN A 61 52.65 -97.06 REMARK 500 7 ALA A 98 164.58 66.78 REMARK 500 7 ARG A 112 179.42 58.61 REMARK 500 7 HIS A 117 -38.55 -137.19 REMARK 500 7 HIS A 118 -7.52 -160.57 REMARK 500 8 ASN A 61 54.94 -96.91 REMARK 500 8 ALA A 98 166.14 65.85 REMARK 500 8 ARG A 112 -40.76 -164.36 REMARK 500 9 ASN A 61 54.84 -97.62 REMARK 500 9 ALA A 98 170.71 65.23 REMARK 500 10 ASN A 61 55.01 -96.12 REMARK 500 10 ALA A 98 151.32 67.92 REMARK 500 10 LEU A 115 -18.59 -142.65 REMARK 500 10 HIS A 117 -46.41 -139.31 REMARK 500 11 ALA A 19 108.33 -55.44 REMARK 500 11 ASN A 61 54.55 -97.18 REMARK 500 11 ALA A 98 176.88 65.37 REMARK 500 11 ARG A 112 -58.52 56.71 REMARK 500 REMARK 500 THIS ENTRY HAS 92 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 1 ARG A 104 0.08 SIDE CHAIN REMARK 500 2 ARG A 92 0.08 SIDE CHAIN REMARK 500 3 ARG A 44 0.08 SIDE CHAIN REMARK 500 9 ARG A 55 0.11 SIDE CHAIN REMARK 500 17 ARG A 92 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36339 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF FOLD-U NOMUR; DE NOVO DESIGNED PROTEIN REMARK 900 WITH AN ASYMMETRIC ALL-ALPHA TOPOLOGY DBREF 7BQS A 1 122 PDB 7BQS 7BQS 1 122 SEQRES 1 A 122 GLY GLU THR LYS ALA LYS ALA ALA GLN GLU ALA LEU ARG SEQRES 2 A 122 ALA ALA ARG GLU GLN ALA THR THR PRO GLU ALA GLN LYS SEQRES 3 A 122 ALA LEU GLU GLU LEU GLU LYS VAL LEU LYS THR ALA SER SEQRES 4 A 122 PRO GLU GLN TRP ARG GLN ALA ALA GLU LYS ILE PHE GLU SEQRES 5 A 122 ALA PHE ARG GLU ALA SER ASN GLY ASN THR GLU LYS ALA SEQRES 6 A 122 LYS LYS LEU LEU GLU GLU ALA ALA ARG THR ALA GLY ALA SEQRES 7 A 122 SER PRO GLU ILE ILE LYS LYS LEU ALA SER ALA LEU GLU SEQRES 8 A 122 ARG LEU ALA GLU GLU GLY ALA ALA LYS GLU ALA ALA ARG SEQRES 9 A 122 GLN ALA GLU GLU VAL ARG LYS ARG GLY SER LEU GLU HIS SEQRES 10 A 122 HIS HIS HIS HIS HIS HELIX 1 AA1 THR A 3 ALA A 19 1 17 HELIX 2 AA2 THR A 21 LYS A 36 1 16 HELIX 3 AA3 SER A 39 ASN A 59 1 21 HELIX 4 AA4 ASN A 61 GLY A 77 1 17 HELIX 5 AA5 SER A 79 GLU A 96 1 18 HELIX 6 AA6 LYS A 100 ARG A 112 1 13 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