HEADER ANTITOXIN/DNA 19-JAN-22 7WNR TITLE DATA-DRIVEN HADDOCK MODEL OF MYCOBACTERIAL NMAZE6-OPERATOR DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(P*CP*CP*GP*GP*TP*TP*AP*TP*AP*CP*TP*AP*TP*CP*TP*GP*TP*A)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(P*TP*AP*CP*AP*GP*AP*TP*AP*GP*TP*AP*TP*AP*AP*CP*CP*GP*G)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ANTITOXIN MAZE6; COMPND 13 CHAIN: B, C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 EXPRESSION_SYSTEM: CHEMICAL PRODUCTION METAGENOME; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 2495586; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 8 ORGANISM_TAXID: 83332; SOURCE 9 EXPRESSION_SYSTEM: CHEMICAL PRODUCTION METAGENOME; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 2495586; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 13 ORGANISM_TAXID: 83332; SOURCE 14 GENE: MAZE6, MAZE-MT3, RV1991A; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HADDOCK MODEL, MYCOBACTERIAL TA SYSTEM, MAZEF6, MAZE6-DNA COMPLEX, KEYWDS 2 ANTITOXIN, ANTITOXIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR K.KUMARI,S.P.SARMA REVDAT 2 15-MAY-24 7WNR 1 REMARK REVDAT 1 12-OCT-22 7WNR 0 JRNL AUTH K.KUMARI,S.P.SARMA JRNL TITL STRUCTURAL AND MUTATIONAL ANALYSIS OF MAZE6-OPERATOR DNA JRNL TITL 2 COMPLEX PROVIDE INSIGHTS INTO AUTOREGULATION OF JRNL TITL 3 TOXIN-ANTITOXIN SYSTEMS. JRNL REF COMMUN BIOL V. 5 963 2022 JRNL REFN ESSN 2399-3642 JRNL PMID 36109664 JRNL DOI 10.1038/S42003-022-03933-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 3.1, HADDOCK REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7WNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300027046. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM NA NMAZE6, 20 MM NA REMARK 210 POTASSIUM PHOSPHATE, 20 MM NA REMARK 210 SODIUM CHLORIDE, 1 MM NA EDTA, REMARK 210 0.01 % NA SODIUM AZIDE, 0.2 MM REMARK 210 NA DSS, 10 % [U-99% 2H] D2O, 90% REMARK 210 H2O/10% D2O; 0.4 MM [U-99% 15N] REMARK 210 NMAZE6, 20 MM NA POTASSIUM REMARK 210 PHOSPHATE, 20 MM NA SODIUM REMARK 210 CHLORIDE, 1 MM NA EDTA, 0.01 % REMARK 210 NA SODIUM AZIDE, 0.2 MM NA DSS, REMARK 210 10 % [U-99% 2H] D2O, 90% H2O/10% REMARK 210 D2O; 0.4 MM [U-99% 13C; U-99% REMARK 210 15N] NMAZE6, 20 MM NA POTASSIUM REMARK 210 PHOSPHATE, 20 MM NA SODIUM REMARK 210 CHLORIDE, 1 MM NA EDTA, 0.01 % REMARK 210 NA SODIUM AZIDE, 0.2 MM NA DSS, REMARK 210 10 % [U-99% 2H] D2O, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CC(CO)NH; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D H(CCO)NH; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY; 13C, 15N REMARK 210 SIMULTANEOUSEDITED NOESY; 3D REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AGILENT DDS2 600MHZ REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ 4.2, NMRPIPE, CCPNMR REMARK 210 ANALYSIS, CYANA REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH FAVORABLE NON REMARK 210 -BOND ENERGY 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, B, C 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 1-4 REMARK 465 RES C SSSEQI REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 SER C 1 REMARK 465 GLY C 2 REMARK 465 SER C 3 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 H3' DG D 27 HH21 ARG B 29 1.14 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 PRO B 11 -173.12 -67.10 REMARK 500 1 PRO C 11 -147.85 -73.35 REMARK 500 2 MET B 27 -156.58 -120.72 REMARK 500 2 ALA C 7 76.64 -108.87 REMARK 500 2 MET C 27 -160.66 -121.67 REMARK 500 2 SER C 28 -169.64 -103.02 REMARK 500 3 PRO B 11 -168.15 -68.44 REMARK 500 3 PRO C 11 -147.47 -73.60 REMARK 500 4 MET B 27 -167.21 -124.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7WJ0 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF NMAZE6 REMARK 900 RELATED ID: 51227 RELATED DB: BMRB DBREF 7WNR A 1 18 PDB 7WNR 7WNR 1 18 DBREF 7WNR D 19 36 PDB 7WNR 7WNR 19 36 DBREF 7WNR B 4 52 UNP P9WJ87 MAZE6_MYCTU 1 49 DBREF 7WNR C 4 52 UNP P9WJ87 MAZE6_MYCTU 1 49 SEQADV 7WNR SER B 1 UNP P9WJ87 EXPRESSION TAG SEQADV 7WNR GLY B 2 UNP P9WJ87 EXPRESSION TAG SEQADV 7WNR SER B 3 UNP P9WJ87 EXPRESSION TAG SEQADV 7WNR SER C 1 UNP P9WJ87 EXPRESSION TAG SEQADV 7WNR GLY C 2 UNP P9WJ87 EXPRESSION TAG SEQADV 7WNR SER C 3 UNP P9WJ87 EXPRESSION TAG SEQRES 1 A 18 DC DC DG DG DT DT DA DT DA DC DT DA DT SEQRES 2 A 18 DC DT DG DT DA SEQRES 1 D 18 DT DA DC DA DG DA DT DA DG DT DA DT DA SEQRES 2 D 18 DA DC DC DG DG SEQRES 1 B 52 SER GLY SER MET LYS THR ALA ILE SER LEU PRO ASP GLU SEQRES 2 B 52 THR PHE ASP ARG VAL SER ARG ARG ALA SER GLU LEU GLY SEQRES 3 B 52 MET SER ARG SER GLU PHE PHE THR LYS ALA ALA GLN ARG SEQRES 4 B 52 TYR LEU HIS GLU LEU ASP ALA GLN LEU LEU THR GLY GLN SEQRES 1 C 52 SER GLY SER MET LYS THR ALA ILE SER LEU PRO ASP GLU SEQRES 2 C 52 THR PHE ASP ARG VAL SER ARG ARG ALA SER GLU LEU GLY SEQRES 3 C 52 MET SER ARG SER GLU PHE PHE THR LYS ALA ALA GLN ARG SEQRES 4 C 52 TYR LEU HIS GLU LEU ASP ALA GLN LEU LEU THR GLY GLN HELIX 1 AA1 PRO B 11 GLY B 26 1 16 HELIX 2 AA2 SER B 28 GLY B 51 1 24 HELIX 3 AA3 ASP C 12 GLY C 26 1 15 HELIX 4 AA4 SER C 28 THR C 50 1 23 SHEET 1 AA1 2 LYS B 5 SER B 9 0 SHEET 2 AA1 2 LYS C 5 SER C 9 -1 O ILE C 8 N THR B 6 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