HEADER RNA BINDING PROTEIN 13-JAN-20 6TWR TITLE STRUCTURE OF A CONSTITUTIVELY ACTIVE CAT-PRD1 MUTANT OF THE TITLE 2 ANTITERMINATOR LICT PROTEIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-GLUCOSIDE BGL OPERON ANTITERMINATOR BGLG FAMILY; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PRD DOMAIN-CONTAINING PROTEIN,TRANSCRIPTION ANTITERMINATOR COMPND 5 LICT; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: B4122_4365, B4417_2239, ETA10_20555, ETL41_11840, FVD40_12670; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ANTITERMINATION PROTEIN, BACILLUS SUBTILIS, DIMERIC PROTEIN, KEYWDS 2 REGULATED BY THE PTS, HISTIDINE PHOSPHORYLATION, ACTIVATED MUTANT, KEYWDS 3 RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.DEMENE,N.DECLERCK,Y.YINSHAN REVDAT 3 14-JUN-23 6TWR 1 REMARK REVDAT 2 05-MAY-21 6TWR 1 JRNL REVDAT 1 14-APR-21 6TWR 0 JRNL AUTH Y.YANG,J.GRACY,N.DECLERCK,H.DEMENE JRNL TITL RESOLVING THE ACTIVATION MECHANISM OF THE D99N JRNL TITL 2 ANTITERMINATOR LICT PROTEIN. JRNL REF J.STRUCT.BIOL. V. 213 07730 2021 JRNL REFN ESSN 1095-8657 JRNL PMID 33781896 JRNL DOI 10.1016/J.JSB.2021.107730 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.YANG,N.DECLERCK,H.DEMENE REMARK 1 TITL NMR CHEMICAL SHIFT ASSIGNMENT OF A CONSTITUTIVELY ACTIVE REMARK 1 TITL 2 FRAGMENT OF THE ANTITERMINATION PROTEIN LICT. REMARK 1 REF BIOMOL NMR ASSIGN 2019 REMARK 1 REFN ESSN 1874-270X REMARK 1 DOI 10.1007/S12104-019-09914-W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS XPLOR REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292105967. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 303 REMARK 210 PH : 8; 6.4 REMARK 210 IONIC STRENGTH : 200; 200 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.380 MM [U-99% 13C; U-99% 15N] REMARK 210 CAT-PRD1 MUTANT, 200 MM SODIUM REMARK 210 CHLORIDE, 10 MM NA TRIS, 0.2 MM REMARK 210 EDTA, 0.2 MM BENZAMIDINE, 1 MM REMARK 210 DTT, 90% H2O/10% D2O; 1 MM [U-99% REMARK 210 15N] LICT CAT-PRD1 MUTANT, 200 REMARK 210 MM SODIUM CHLORIDE, 0.5 MM EDTA, REMARK 210 0.2 MM BENZAMIDINE, 10 MM TRIS, REMARK 210 1 MM DTT, 90% H2O/10% D2O; 0.8 REMARK 210 MM [U-99% 13C; U-99% 15N] LICT REMARK 210 CAT-PRD1 MUTANT, 200 MM SODIUM REMARK 210 CHLORIDE, 10 MM TRIS, 0.5 MM REMARK 210 EDTA, 0.2 MM BENZAMIDINE, 1 MM REMARK 210 DTT, 90% H2O/10% D2O; 0.8 MM [U- REMARK 210 99% 13C; U-99% 15N] LICT CAT- REMARK 210 PRD1 MUTANT, 10 MM SODIUM REMARK 210 PHOSPHATE, 200 MM NACL, 0.2 MM REMARK 210 EDTA, 0.2 MM DTT, 0.2 MM REMARK 210 BENZAMIDINE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D CBCA(CO)NH; 3D HN(CO) REMARK 210 CA; 3D HNCA; 2D 1H-13C FILTERED REMARK 210 NOESY; 3D HNCO; 3D HNCACB; 3D REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.6, CYANA 3.0, GIFA REMARK 210 5.0, CNS 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS B 170 REMARK 465 HIS B 171 REMARK 465 HIS B 172 REMARK 465 HIS B 173 REMARK 465 HIS B 174 REMARK 465 HIS B 175 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 OE2 GLU A 21 HZ1 LYS B 46 1.55 REMARK 500 HZ3 LYS A 53 OD2 ASP A 54 1.58 REMARK 500 HZ2 LYS A 46 OE1 GLU B 21 1.59 REMARK 500 HZ3 LYS A 58 OD2 ASP B 91 1.60 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 166 115.27 72.56 REMARK 500 1 PHE B 31 109.51 -58.60 REMARK 500 1 GLN B 32 -11.18 79.23 REMARK 500 1 LEU B 165 37.47 -99.69 REMARK 500 1 ASN B 166 173.26 68.51 REMARK 500 2 ASN A 8 -175.40 -177.21 REMARK 500 2 TYR A 126 42.81 -105.85 REMARK 500 2 ARG B 27 107.86 -54.88 REMARK 500 2 TYR B 126 50.02 -111.67 REMARK 500 3 GLN A 32 12.68 80.05 REMARK 500 3 LEU A 168 96.55 173.99 REMARK 500 3 SER B 56 48.43 -100.92 REMARK 500 3 SER B 92 9.81 -67.68 REMARK 500 3 ILE B 93 -35.74 -133.22 REMARK 500 3 TYR B 126 65.81 -100.79 REMARK 500 4 GLU A 167 110.29 -26.91 REMARK 500 4 ASN B 8 -175.47 -173.53 REMARK 500 4 ASN B 166 99.92 -53.26 REMARK 500 4 GLU B 167 110.91 52.24 REMARK 500 5 TYR A 126 30.32 -93.18 REMARK 500 5 ASP B 40 99.70 -64.39 REMARK 500 5 ILE B 93 -33.54 -163.74 REMARK 500 5 TYR B 126 31.01 -90.21 REMARK 500 6 ARG A 27 98.89 -57.79 REMARK 500 6 GLU A 167 73.25 63.59 REMARK 500 6 LEU A 168 99.89 -171.28 REMARK 500 6 TYR B 126 45.36 -106.21 REMARK 500 6 GLU B 167 104.13 -51.28 REMARK 500 7 ASN A 8 -179.27 -170.07 REMARK 500 7 SER A 56 42.40 -102.56 REMARK 500 7 ASN A 166 96.01 -53.49 REMARK 500 8 TYR A 126 44.97 -109.00 REMARK 500 8 GLU A 167 108.34 -32.62 REMARK 500 9 ARG A 27 105.09 -59.16 REMARK 500 9 SER A 56 47.45 -100.82 REMARK 500 9 ASN A 166 106.96 -48.66 REMARK 500 9 GLU A 167 147.30 -172.98 REMARK 500 10 LEU B 165 41.67 -152.56 REMARK 500 10 ASN B 166 109.01 -26.69 REMARK 500 11 TYR A 126 62.87 -105.58 REMARK 500 11 ASN B 8 -178.66 -175.29 REMARK 500 12 SER A 56 49.93 -146.44 REMARK 500 12 TYR A 126 47.86 -106.02 REMARK 500 12 ASN A 166 102.65 -49.98 REMARK 500 12 LEU A 168 39.99 -90.01 REMARK 500 12 PHE B 31 108.83 -52.11 REMARK 500 13 ASN A 8 -174.52 -170.16 REMARK 500 14 ILE A 66 109.39 -51.44 REMARK 500 14 PHE B 31 109.10 -56.59 REMARK 500 14 GLN B 32 34.61 71.49 REMARK 500 REMARK 500 THIS ENTRY HAS 73 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 3 ARG A 43 0.10 SIDE CHAIN REMARK 500 6 ARG A 43 0.08 SIDE CHAIN REMARK 500 8 ARG A 107 0.13 SIDE CHAIN REMARK 500 9 ARG A 43 0.09 SIDE CHAIN REMARK 500 11 ARG B 43 0.08 SIDE CHAIN REMARK 500 12 ARG A 43 0.08 SIDE CHAIN REMARK 500 16 ARG B 43 0.09 SIDE CHAIN REMARK 500 18 ARG A 107 0.07 SIDE CHAIN REMARK 500 20 ARG A 43 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TLV RELATED DB: PDB REMARK 900 NATIVE FORM OF PRDS REMARK 900 RELATED ID: 27893 RELATED DB: BMRB REMARK 900 RELATED ID: 1H99 RELATED DB: PDB REMARK 900 PHOSPHOMIMETIC MUTANT OF PRD2 DOMAIN REMARK 900 RELATED ID: 1L1C RELATED DB: PDB REMARK 900 CAT DOMAIN COMPLEXED TO ARN DBREF1 6TWR A 1 167 UNP A0A063XFU4_BACIU DBREF2 6TWR A A0A063XFU4 1 167 DBREF1 6TWR B 1 167 UNP A0A063XFU4_BACIU DBREF2 6TWR B A0A063XFU4 1 167 SEQADV 6TWR ASN A 99 UNP A0A063XFU ASP 99 CONFLICT SEQADV 6TWR LEU A 168 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR GLN A 169 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS A 170 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS A 171 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS A 172 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS A 173 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS A 174 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS A 175 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR ASN B 99 UNP A0A063XFU ASP 99 ENGINEERED MUTATION SEQADV 6TWR LEU B 168 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR GLN B 169 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS B 170 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS B 171 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS B 172 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS B 173 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS B 174 UNP A0A063XFU EXPRESSION TAG SEQADV 6TWR HIS B 175 UNP A0A063XFU EXPRESSION TAG SEQRES 1 A 175 MET LYS ILE ALA LYS VAL ILE ASN ASN ASN VAL ILE SER SEQRES 2 A 175 VAL VAL ASN GLU GLN GLY LYS GLU LEU VAL VAL MET GLY SEQRES 3 A 175 ARG GLY LEU ALA PHE GLN LYS LYS SER GLY ASP ASP VAL SEQRES 4 A 175 ASP GLU ALA ARG ILE GLU LYS VAL PHE THR LEU ASP ASN SEQRES 5 A 175 LYS ASP VAL SER GLU LYS PHE LYS THR LEU LEU TYR ASP SEQRES 6 A 175 ILE PRO ILE GLU CYS MET GLU VAL SER GLU GLU ILE ILE SEQRES 7 A 175 SER TYR ALA LYS LEU GLN LEU GLY LYS LYS LEU ASN ASP SEQRES 8 A 175 SER ILE TYR VAL SER LEU THR ASN HIS ILE ASN PHE ALA SEQRES 9 A 175 ILE GLN ARG ASN GLN LYS GLY LEU ASP ILE LYS ASN ALA SEQRES 10 A 175 LEU LEU TRP GLU THR LYS ARG LEU TYR LYS ASP GLU PHE SEQRES 11 A 175 ALA ILE GLY LYS GLU ALA LEU VAL MET VAL LYS ASN LYS SEQRES 12 A 175 THR GLY VAL SER LEU PRO GLU ASP GLU ALA GLY PHE ILE SEQRES 13 A 175 ALA LEU HIS ILE VAL ASN ALA GLU LEU ASN GLU LEU GLN SEQRES 14 A 175 HIS HIS HIS HIS HIS HIS SEQRES 1 B 175 MET LYS ILE ALA LYS VAL ILE ASN ASN ASN VAL ILE SER SEQRES 2 B 175 VAL VAL ASN GLU GLN GLY LYS GLU LEU VAL VAL MET GLY SEQRES 3 B 175 ARG GLY LEU ALA PHE GLN LYS LYS SER GLY ASP ASP VAL SEQRES 4 B 175 ASP GLU ALA ARG ILE GLU LYS VAL PHE THR LEU ASP ASN SEQRES 5 B 175 LYS ASP VAL SER GLU LYS PHE LYS THR LEU LEU TYR ASP SEQRES 6 B 175 ILE PRO ILE GLU CYS MET GLU VAL SER GLU GLU ILE ILE SEQRES 7 B 175 SER TYR ALA LYS LEU GLN LEU GLY LYS LYS LEU ASN ASP SEQRES 8 B 175 SER ILE TYR VAL SER LEU THR ASN HIS ILE ASN PHE ALA SEQRES 9 B 175 ILE GLN ARG ASN GLN LYS GLY LEU ASP ILE LYS ASN ALA SEQRES 10 B 175 LEU LEU TRP GLU THR LYS ARG LEU TYR LYS ASP GLU PHE SEQRES 11 B 175 ALA ILE GLY LYS GLU ALA LEU VAL MET VAL LYS ASN LYS SEQRES 12 B 175 THR GLY VAL SER LEU PRO GLU ASP GLU ALA GLY PHE ILE SEQRES 13 B 175 ALA LEU HIS ILE VAL ASN ALA GLU LEU ASN GLU LEU GLN SEQRES 14 B 175 HIS HIS HIS HIS HIS HIS HELIX 1 AA1 LYS A 58 ILE A 66 1 9 HELIX 2 AA2 PRO A 67 GLY A 86 1 20 HELIX 3 AA3 ASP A 91 GLY A 111 1 21 HELIX 4 AA4 LEU A 118 TYR A 126 1 9 HELIX 5 AA5 LYS A 127 THR A 144 1 18 HELIX 6 AA6 PRO A 149 GLU A 164 1 16 HELIX 7 AA7 GLU B 57 ILE B 66 1 10 HELIX 8 AA8 PRO B 67 GLY B 86 1 20 HELIX 9 AA9 ASP B 91 GLY B 111 1 21 HELIX 10 AB1 LEU B 118 TYR B 126 1 9 HELIX 11 AB2 LYS B 127 GLY B 145 1 19 HELIX 12 AB3 PRO B 149 GLU B 164 1 16 SHEET 1 AA1 8 LYS A 2 VAL A 6 0 SHEET 2 AA1 8 VAL A 11 VAL A 15 -1 O SER A 13 N LYS A 5 SHEET 3 AA1 8 GLU A 21 GLY A 26 -1 O LEU A 22 N VAL A 14 SHEET 4 AA1 8 ILE A 44 ASP A 51 -1 O LYS A 46 N MET A 25 SHEET 5 AA1 8 LYS B 46 ASP B 51 -1 O VAL B 47 N ASP A 51 SHEET 6 AA1 8 GLU B 21 MET B 25 -1 N MET B 25 O LYS B 46 SHEET 7 AA1 8 VAL B 11 VAL B 15 -1 N ILE B 12 O VAL B 24 SHEET 8 AA1 8 LYS B 2 VAL B 6 -1 N LYS B 5 O SER B 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