HEADER DE NOVO PROTEIN 25-MAR-20 7BQQ TITLE SOLUTION NMR STRUCTURE OF FOLD-Z GOGY; DE NOVO DESIGNED PROTEIN WITH TITLE 2 AN ASYMMETRIC ALL-ALPHA TOPOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOGY; 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,K.SAKUMA,T.KOSUGI,R.KOGA,N.KOGA REVDAT 4 15-MAY-24 7BQQ 1 REMARK REVDAT 3 10-JAN-24 7BQQ 1 JRNL REVDAT 2 14-JUN-23 7BQQ 1 REMARK REVDAT 1 07-APR-21 7BQQ 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 7BQQ 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_1300016043. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.52 REMARK 210 IONIC STRENGTH : 60 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-100% 13C; U-100% 15N] REMARK 210 GOGY, 6.8 MM POTASSIUM PHOSPHATE, REMARK 210 3.20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 95% H2O/5% D2O; REMARK 210 0.2 MM [U-100% 13C; U-100% 15N] REMARK 210 GOGY, 6.8 MM POTASSIUM PHOSPHATE, REMARK 210 3.2 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 7 MG/ML PF1 REMARK 210 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 BEST-HNCO; 3D BEST- REMARK 210 HNCACB; 3D HCCH-TOCSY ALIPHATIC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-15N HSQC IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 950 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 2.01.14, NMRVIEW 9.0, CYANA 3.98, REMARK 210 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 14 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 8 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 11 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 14 ARG A 113 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 16 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 65 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 HIS A 126 27.92 -73.36 REMARK 500 2 GLU A 124 -52.54 -125.17 REMARK 500 2 HIS A 125 -33.10 61.22 REMARK 500 3 HIS A 128 -42.63 -148.72 REMARK 500 4 GLU A 124 -64.22 -140.45 REMARK 500 5 ASP A 83 69.25 -102.66 REMARK 500 8 HIS A 129 129.25 60.31 REMARK 500 9 HIS A 128 -161.85 53.93 REMARK 500 10 HIS A 128 161.83 60.35 REMARK 500 11 ASP A 83 78.80 -102.73 REMARK 500 11 HIS A 128 -51.24 -152.92 REMARK 500 11 HIS A 129 173.51 56.34 REMARK 500 12 ASP A 2 14.32 59.65 REMARK 500 12 SER A 122 -152.46 51.32 REMARK 500 13 ASP A 83 74.35 -104.07 REMARK 500 14 GLU A 124 77.02 -114.13 REMARK 500 14 HIS A 127 86.24 51.15 REMARK 500 14 HIS A 129 -47.39 -141.73 REMARK 500 15 LEU A 123 48.39 -144.98 REMARK 500 15 HIS A 125 -165.95 53.83 REMARK 500 15 HIS A 126 -48.16 67.42 REMARK 500 16 ASP A 2 -10.66 -141.80 REMARK 500 16 ASP A 83 72.48 -102.75 REMARK 500 16 GLU A 124 -69.52 -123.40 REMARK 500 16 HIS A 125 -32.21 57.77 REMARK 500 16 HIS A 128 161.14 65.45 REMARK 500 17 HIS A 127 43.72 -78.81 REMARK 500 18 ASP A 83 76.45 -100.03 REMARK 500 19 SER A 122 176.81 63.51 REMARK 500 20 GLU A 124 -37.13 -130.83 REMARK 500 20 HIS A 129 -177.73 57.68 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 7 ARG A 92 0.09 SIDE CHAIN REMARK 500 11 ARG A 117 0.08 SIDE CHAIN REMARK 500 12 ARG A 74 0.08 SIDE CHAIN REMARK 500 18 ARG A 74 0.09 SIDE CHAIN REMARK 500 19 ARG A 92 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36337 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF FOLD-Z GOGY; DE NOVO DESIGNED PROTEIN REMARK 900 WITH AN ASYMMETRIC ALL-ALPHA TOPOLOGY DBREF 7BQQ A 1 130 PDB 7BQQ 7BQQ 1 130 SEQRES 1 A 130 GLY ASP GLU ARG LYS LEU GLU GLU VAL THR GLU GLU MET SEQRES 2 A 130 ARG LYS MET ALA GLU ASN MET ASP GLY GLN ASP PRO GLU SEQRES 3 A 130 LYS VAL LYS GLU ILE VAL ARG ARG ALA LEU GLN GLN MET SEQRES 4 A 130 ALA ASN ASP ASN PRO GLU VAL SER GLU GLN LEU ARG GLU SEQRES 5 A 130 LEU ALA LYS ARG LYS GLY THR SER PRO SER GLU VAL ILE SEQRES 6 A 130 LYS ASP LEU ALA GLU GLN VAL TRP ARG ALA MET GLU ARG SEQRES 7 A 130 ALA ARG GLU GLY ASP LYS ASP THR ALA ARG GLU LEU ILE SEQRES 8 A 130 ARG LYS PHE ALA ASP ASP LEU GLY ILE SER PRO GLU GLN SEQRES 9 A 130 VAL LYS LYS PHE ILE LYS ILE MET ARG GLU VAL GLN ARG SEQRES 10 A 130 LYS GLU ASP GLY SER LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASP A 2 MET A 20 1 19 HELIX 2 AA2 ASP A 24 ASN A 43 1 20 HELIX 3 AA3 ASN A 43 GLY A 58 1 16 HELIX 4 AA4 GLU A 63 GLY A 82 1 20 HELIX 5 AA5 ASP A 83 GLY A 99 1 17 HELIX 6 AA6 SER A 101 ARG A 117 1 17 HELIX 7 AA7 LYS A 118 ASP A 120 5 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