HEADER SPLICING 15-DEC-21 7QIL TITLE SOLUTION NMR STRUCTURE OF HALOPHILIC DNAE INTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNAE INTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC; SOURCE 3 ORGANISM_TAXID: 1177; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN SPLICING, SEGMENTAL ISOTOPIC LABELING, CONDITIONAL PROTEIN KEYWDS 2 SPLICING, PROTEIN ENGINEERING, SPLICING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.A.HEIKKINEN,S.A.ARANKO,H.IWAI REVDAT 1 27-APR-22 7QIL 0 JRNL AUTH H.A.HEIKKINEN,A.S.ARANKO,H.IWAI JRNL TITL THE NMR STRUCTURE OF THE ENGINEERED HALOPHILIC DNAE INTEIN JRNL TITL 2 FOR SEGMENTAL ISOTOPIC LABELING USING CONDITIONAL PROTEIN JRNL TITL 3 SPLICING. JRNL REF J.MAGN.RESON. V. 338 07195 2022 JRNL REFN ISSN 0022-2364 JRNL PMID 35398651 JRNL DOI 10.1016/J.JMR.2022.107195 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 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 7QIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119718. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 2 M NACL REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 1.6 MM [20% 13C], [U-15N] DNAE REMARK 210 INTEIN, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 3D 1H-13C NOESY; 3D 1H-15N NOESY; REMARK 210 3D HCCH-COSY; 3D CBCA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HN(CO)CA; 3D REMARK 210 HNCACB; 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.2, CYANA, CCPNMR REMARK 210 ANALYSIS REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 52 HG SER A 113 1.59 REMARK 500 HG SER A 32 OD2 ASP A 124 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 67 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 14 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 16 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 18 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 19 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 19 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.5 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 TYR A 13 -3.85 -145.77 REMARK 500 1 MET A 95 136.26 -36.29 REMARK 500 1 ASP A 98 42.98 -77.87 REMARK 500 1 SER A 123 -82.19 -77.33 REMARK 500 2 GLU A 27 32.72 -90.28 REMARK 500 2 THR A 29 90.56 -64.17 REMARK 500 2 GLU A 91 34.75 70.47 REMARK 500 2 THR A 103 -9.12 67.62 REMARK 500 3 THR A 29 97.89 -61.35 REMARK 500 3 GLU A 52 112.77 -160.08 REMARK 500 3 THR A 103 -27.74 -147.76 REMARK 500 3 ASP A 124 -28.75 -154.07 REMARK 500 4 GLU A 12 -87.35 -82.45 REMARK 500 4 ALA A 45 11.88 -145.66 REMARK 500 4 THR A 111 -4.53 -144.08 REMARK 500 4 HIS A 125 50.40 39.42 REMARK 500 5 TYR A 13 -34.14 -161.44 REMARK 500 5 ASP A 102 49.03 -77.47 REMARK 500 5 ASP A 124 -10.74 -150.91 REMARK 500 5 HIS A 125 19.75 57.55 REMARK 500 5 ASP A 131 -5.94 66.44 REMARK 500 6 ASP A 98 40.60 -69.99 REMARK 500 6 THR A 111 -9.60 -143.28 REMARK 500 6 ASP A 131 -7.76 63.72 REMARK 500 6 PHE A 133 -123.85 -137.69 REMARK 500 7 THR A 29 88.06 -60.66 REMARK 500 7 ASP A 98 -13.57 -43.85 REMARK 500 7 HIS A 125 -0.89 52.06 REMARK 500 8 TYR A 13 -7.39 -142.30 REMARK 500 8 ASP A 124 -13.54 -155.31 REMARK 500 8 ASP A 131 -0.07 68.36 REMARK 500 9 THR A 29 99.71 -69.05 REMARK 500 9 THR A 103 -38.89 -147.61 REMARK 500 9 ASP A 131 -2.99 63.00 REMARK 500 10 TYR A 13 -10.30 -154.94 REMARK 500 10 GLU A 27 31.83 -81.73 REMARK 500 10 ASP A 98 59.81 -68.86 REMARK 500 10 HIS A 125 1.88 54.99 REMARK 500 10 PHE A 133 -134.70 -143.73 REMARK 500 11 TYR A 13 -12.35 -143.47 REMARK 500 11 ARG A 50 29.80 -141.02 REMARK 500 11 LYS A 70 4.92 -69.97 REMARK 500 11 ASP A 98 69.38 -65.22 REMARK 500 11 SER A 100 179.35 -56.07 REMARK 500 11 THR A 103 26.98 -71.25 REMARK 500 11 THR A 111 -10.75 -143.53 REMARK 500 12 ALA A 1 86.24 -61.95 REMARK 500 12 THR A 6 94.42 -65.00 REMARK 500 12 SER A 38 109.48 -59.81 REMARK 500 12 ALA A 45 -33.48 -144.61 REMARK 500 REMARK 500 THIS ENTRY HAS 93 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 99 SER A 100 2 -149.10 REMARK 500 GLY A 132 PHE A 133 12 -147.91 REMARK 500 ALA A 68 THR A 69 14 148.43 REMARK 500 ARG A 96 VAL A 97 18 149.24 REMARK 500 ASP A 131 GLY A 132 19 148.78 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 5 ARG A 96 0.09 SIDE CHAIN REMARK 500 20 TYR A 4 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34695 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF HALOPHILIC DNAE INTEIN DBREF 7QIL A -2 137 PDB 7QIL 7QIL -2 137 SEQRES 1 A 140 SER GLY GLY ALA LEU SER TYR ASP THR GLU ILE LEU THR SEQRES 2 A 140 THR GLU TYR GLY LEU LEU PRO ILE GLY ASP ILE VAL GLU SEQRES 3 A 140 SER GLU THR GLU CYS THR VAL TYR SER VAL ASP SER ASP SEQRES 4 A 140 GLY SER THR TYR THR GLN GLY VAL ALA GLU TRP HIS ASP SEQRES 5 A 140 ARG GLY GLU GLN GLU VAL PHE GLU TYR CYS LEU GLU ASP SEQRES 6 A 140 GLY SER THR ILE ARG ALA THR LYS ASP HIS LYS PHE MET SEQRES 7 A 140 THR THR ASP GLY GLU MET LEU PRO ILE ASP GLU ILE PHE SEQRES 8 A 140 GLU SER GLU LEU ASP LEU MET ARG VAL ASP SER SER GLY SEQRES 9 A 140 ASP THR LYS ILE ALA THR ARG GLU TYR THR GLY SER GLU SEQRES 10 A 140 ASP VAL TYR ASP ILE GLY VAL GLU SER ASP HIS ASN PHE SEQRES 11 A 140 ALA LEU SER ASP GLY PHE ILE ALA SER ASN HELIX 1 AA1 ILE A 18 SER A 24 1 7 HELIX 2 AA2 ILE A 84 SER A 90 1 7 SHEET 1 AA1 5 LEU A 2 SER A 3 0 SHEET 2 AA1 5 THR A 65 ALA A 68 -1 O ARG A 67 N SER A 3 SHEET 3 AA1 5 GLU A 46 LEU A 60 -1 N TYR A 58 O ILE A 66 SHEET 4 AA1 5 ILE A 105 GLY A 120 -1 O GLU A 109 N GLU A 57 SHEET 5 AA1 5 LEU A 2 SER A 3 -1 N LEU A 2 O TYR A 117 SHEET 1 AA2 3 GLY A 14 PRO A 17 0 SHEET 2 AA2 3 GLU A 7 THR A 10 -1 N ILE A 8 O LEU A 16 SHEET 3 AA2 3 LEU A 129 SER A 130 -1 O SER A 130 N GLU A 7 SHEET 1 AA3 2 THR A 29 VAL A 33 0 SHEET 2 AA3 2 THR A 39 GLY A 43 -1 O TYR A 40 N SER A 32 SHEET 1 AA4 2 LYS A 73 MET A 75 0 SHEET 2 AA4 2 MET A 81 PRO A 83 -1 O LEU A 82 N PHE A 74 SHEET 1 AA5 2 ASN A 126 PHE A 127 0 SHEET 2 AA5 2 ALA A 135 SER A 136 -1 O ALA A 135 N PHE A 127 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