HEADER TRANSCRIPTION 04-JAN-24 8RLZ TITLE NMR SOLUTION STRUCTURE OF THE N-TERMINAL CYTOPLASMIC DOMAIN, DDVANT, TITLE 2 OF THE MEMBRANE ANTISIGMA FACTOR DDVA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTISIGMA FACTOR DDVA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTISIGMA FACTOR DDVA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYXOCOCCUS XANTHUS; SOURCE 3 ORGANISM_TAXID: 34; SOURCE 4 STRAIN: DK1050; SOURCE 5 GENE: I5Q59_35855; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MEMBRANE ANTISIGMA, ZINC-ASSOCIATED ANTISIGMA DOMAIN, ECF SIGMA KEYWDS 2 BINDING DOMAIN, THREE-HELIX BUNDLE, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.PANTOJA-UCEDA,S.PADMANABHAN REVDAT 1 06-NOV-24 8RLZ 0 JRNL AUTH D.BERNAL-BERNAL,D.PANTOJA-UCEDA,J.P.LOPEZ-ALONSO, JRNL AUTH 2 A.LOPEZ-ROJO,J.A.LOPEZ-RUIZ,M.GALBIS-MARTINEZ, JRNL AUTH 3 B.OCHOA-LIZARRALDE,I.TASCON,M.ELIAS-ARNANZ, JRNL AUTH 4 I.UBARRETXENA-BELANDIA,S.PADMANABHAN JRNL TITL STRUCTURAL BASIS FOR REGULATION OF A CBASS-CRISPR-CAS JRNL TITL 2 DEFENSE ISLAND BY A TRANSMEMBRANE ANTI-SIGMA FACTOR AND ITS JRNL TITL 3 ECF SIGMA PARTNER. JRNL REF SCI ADV V. 10 P1053 2024 JRNL REFN ESSN 2375-2548 JRNL PMID 39454004 JRNL DOI 10.1126/SCIADV.ADP1053 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 8RLZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135664. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-13C; U-15N] DDVANT, REMARK 210 100 MM SODIUM CHLORIDE, 20 MM REMARK 210 TRIS, 2 MM BETA-MERCAPTOETHANOL, REMARK 210 0.05 % SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; 0.7 MM DDVANT, 100 MM REMARK 210 SODIUM CHLORIDE, 20 MM TRIS, 2 REMARK 210 MM BETA-MERCAPTOETHANOL, 0.05 % REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D HNCA; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 H(CCO)NH; 3D (H)CCCONH; 3D HNHA; REMARK 210 3D HBHA(CO)NH; 3D (H)N(COCA)NH; REMARK 210 3D H(MCOCA)NH; 2D NOESY; 2D REMARK 210 TOCSY; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, NMRVIEW, CYANA 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 : 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 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 ASP A 31 105.18 -45.80 REMARK 500 2 ALA A 30 164.39 -48.39 REMARK 500 2 ASP A 31 107.52 -46.20 REMARK 500 2 GLU A 54 -54.43 -142.85 REMARK 500 3 ASP A 31 100.20 -28.64 REMARK 500 3 HIS A 64 10.07 -66.72 REMARK 500 4 ASP A 31 105.68 -47.26 REMARK 500 4 LEU A 48 106.92 -59.09 REMARK 500 5 ASP A 31 102.63 -46.38 REMARK 500 5 ALA A 65 77.26 -104.61 REMARK 500 6 VAL A -6 69.19 -114.75 REMARK 500 6 ASP A 31 102.90 -47.02 REMARK 500 6 TRP A 63 -34.00 -135.39 REMARK 500 7 ALA A 30 165.37 -49.60 REMARK 500 7 ASP A 31 105.64 -47.44 REMARK 500 8 VAL A -6 58.08 35.35 REMARK 500 8 SER A -2 85.64 -65.18 REMARK 500 8 ASP A 31 102.19 -41.76 REMARK 500 8 LEU A 66 66.42 -150.92 REMARK 500 9 ASP A 31 103.20 -27.95 REMARK 500 10 MET A 1 37.88 -71.92 REMARK 500 10 ASP A 31 105.19 -47.32 REMARK 500 11 ASP A 31 105.97 -46.53 REMARK 500 11 GLN A 47 35.25 -99.51 REMARK 500 12 ASP A 31 103.13 -41.36 REMARK 500 12 ALA A 65 -169.48 -78.31 REMARK 500 13 VAL A -6 77.75 -159.78 REMARK 500 13 ALA A 30 165.04 -48.83 REMARK 500 13 ASP A 31 108.10 -46.46 REMARK 500 14 SER A 3 49.66 -99.36 REMARK 500 14 ASP A 31 100.84 -29.95 REMARK 500 15 ALA A 30 164.55 -49.54 REMARK 500 15 ASP A 31 104.16 -45.47 REMARK 500 15 HIS A 64 24.10 -72.29 REMARK 500 15 ARG A 68 39.53 -68.52 REMARK 500 16 ASP A 31 104.24 -43.23 REMARK 500 16 ARG A 55 39.19 -78.60 REMARK 500 17 ASP A 31 102.70 -45.87 REMARK 500 17 ILE A 53 23.86 -141.81 REMARK 500 18 ARG A -4 62.44 -114.42 REMARK 500 18 MET A 1 85.41 -62.44 REMARK 500 18 ASP A 31 106.60 -46.89 REMARK 500 19 ALA A 30 165.18 -49.10 REMARK 500 19 ASP A 31 105.07 -43.03 REMARK 500 20 SER A 2 -34.37 -131.92 REMARK 500 20 SER A 3 -60.75 -130.54 REMARK 500 20 ALA A 30 150.05 -46.58 REMARK 500 20 ASP A 31 104.17 -37.15 REMARK 500 20 ILE A 53 108.20 -53.04 REMARK 500 20 HIS A 64 23.58 -73.06 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 HIS A 28 NE2 92.8 REMARK 620 3 CYS A 32 SG 101.8 135.1 REMARK 620 4 CYS A 35 SG 90.6 116.3 105.8 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34890 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE N-TERMINAL CYTOPLASMIC DOMAIN, DDVANT, REMARK 900 OF THE MEMBRANE ANTISIGMA FACTOR DDVA DBREF1 8RLZ A 1 70 UNP A0A8E4SKQ1_MYXXA DBREF2 8RLZ A A0A8E4SKQ1 1 70 SEQADV 8RLZ GLY A -19 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ SER A -18 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ SER A -17 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ HIS A -16 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ HIS A -15 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ HIS A -14 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ HIS A -13 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ HIS A -12 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ HIS A -11 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ SER A -10 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ SER A -9 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ GLY A -8 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ LEU A -7 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ VAL A -6 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ PRO A -5 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ ARG A -4 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ GLY A -3 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ SER A -2 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ HIS A -1 UNP A0A8E4SKQ EXPRESSION TAG SEQADV 8RLZ MET A 0 UNP A0A8E4SKQ EXPRESSION TAG SEQRES 1 A 90 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 90 VAL PRO ARG GLY SER HIS MET MET SER SER SER PRO CYS SEQRES 3 A 90 ASP GLN LEU GLN SER PHE ALA ASP GLY ASP LEU PRO PRO SEQRES 4 A 90 MET GLU ALA GLN ALA PHE GLY GLN HIS LEU ALA ASP CYS SEQRES 5 A 90 GLU LYS CYS GLN VAL GLU LEU THR ARG LEU LEU GLN LEU SEQRES 6 A 90 ASP GLN LEU GLY ARG GLY TYR ILE GLU ARG HIS GLY PRO SEQRES 7 A 90 VAL ASP ILE PRO TRP HIS ALA LEU PRO ARG ASN ARG HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 AA1 SER A 4 GLY A 15 1 12 HELIX 2 AA2 PRO A 18 PHE A 25 1 8 HELIX 3 AA3 GLY A 26 HIS A 28 5 3 HELIX 4 AA4 CYS A 32 GLN A 47 1 16 LINK SG CYS A 6 ZN ZN A 101 1555 1555 2.46 LINK NE2 HIS A 28 ZN ZN A 101 1555 1555 2.22 LINK SG CYS A 32 ZN ZN A 101 1555 1555 2.46 LINK SG CYS A 35 ZN ZN A 101 1555 1555 2.38 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 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.761 -1.268 1.141 1.00 0.00 ZN ENDMDL MODEL 2 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.799 -1.391 1.183 1.00 0.00 ZN ENDMDL MODEL 3 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.832 -1.340 1.202 1.00 0.00 ZN ENDMDL MODEL 4 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.697 -1.415 0.911 1.00 0.00 ZN ENDMDL MODEL 5 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.672 -1.374 1.014 1.00 0.00 ZN ENDMDL MODEL 6 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.629 -1.303 0.663 1.00 0.00 ZN ENDMDL MODEL 7 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.697 -1.315 1.010 1.00 0.00 ZN ENDMDL MODEL 8 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.676 -1.317 0.886 1.00 0.00 ZN ENDMDL MODEL 9 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.723 -1.015 0.819 1.00 0.00 ZN ENDMDL MODEL 10 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.654 -1.231 0.873 1.00 0.00 ZN ENDMDL MODEL 11 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.808 -1.389 1.206 1.00 0.00 ZN ENDMDL MODEL 12 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.870 -1.101 1.243 1.00 0.00 ZN ENDMDL MODEL 13 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.509 -1.646 0.440 1.00 0.00 ZN ENDMDL MODEL 14 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.792 -0.965 0.780 1.00 0.00 ZN ENDMDL MODEL 15 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.841 -1.427 1.132 1.00 0.00 ZN ENDMDL MODEL 16 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.705 -1.179 0.760 1.00 0.00 ZN ENDMDL MODEL 17 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.766 -1.462 1.001 1.00 0.00 ZN ENDMDL MODEL 18 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.869 -1.318 1.208 1.00 0.00 ZN ENDMDL MODEL 19 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.597 -1.305 0.998 1.00 0.00 ZN ENDMDL MODEL 20 TER 1206 ARG A 70 HETATM 1207 ZN ZN A 101 -7.843 -1.398 1.057 1.00 0.00 ZN ENDMDL CONECT 196 1207 CONECT 507 1207 CONECT 562 1207 CONECT 609 1207 CONECT 1207 196 507 562 609 MASTER 185 0 1 4 0 0 0 6 614 1 5 7 END