HEADER TRANSCRIPTION 11-MAY-23 8SUA TITLE STRUCTURE OF M. BAIXIANGNINGIAE DARR-LIGAND COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DARR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIACEAE; SOURCE 3 ORGANISM_TAXID: 1762; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DARR, MYCOBACTERIA, TFR, TETR, C-DI-AMP, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 3 22-NOV-23 8SUA 1 JRNL REVDAT 2 15-NOV-23 8SUA 1 REMARK REVDAT 1 01-NOV-23 8SUA 0 JRNL AUTH M.A.SCHUMACHER,N.LENT,V.B.CHEN,R.SALINAS JRNL TITL STRUCTURES OF THE DARR TRANSCRIPTION REGULATOR REVEAL UNIQUE JRNL TITL 2 MODES OF SECOND MESSENGER AND DNA BINDING. JRNL REF NAT COMMUN V. 14 7239 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37945601 JRNL DOI 10.1038/S41467-023-42823-0 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1775 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 10.0000 - 3.7600 1.00 2700 148 0.1803 0.1949 REMARK 3 2 3.7600 - 2.9900 1.00 2597 140 0.1766 0.2094 REMARK 3 3 2.9900 - 2.6100 1.00 2566 136 0.1934 0.2280 REMARK 3 4 2.6100 - 2.3700 1.00 2568 139 0.1809 0.1865 REMARK 3 5 2.3700 - 2.2000 1.00 2555 134 0.1708 0.1965 REMARK 3 6 2.2000 - 2.0700 1.00 2555 137 0.1904 0.2385 REMARK 3 7 2.0700 - 1.9700 1.00 2536 137 0.1775 0.1999 REMARK 3 8 1.9700 - 1.8800 1.00 2558 132 0.1821 0.1963 REMARK 3 9 1.8800 - 1.8100 1.00 2528 136 0.1893 0.1992 REMARK 3 10 1.8100 - 1.7500 1.00 2512 134 0.2005 0.2331 REMARK 3 11 1.7500 - 1.6900 1.00 2559 137 0.2322 0.2711 REMARK 3 12 1.6900 - 1.6400 1.00 2503 130 0.1936 0.2365 REMARK 3 13 1.6400 - 1.6000 0.99 2517 135 0.2016 0.2353 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 NULL REMARK 3 ANGLE : 1.150 NULL REMARK 3 CHIRALITY : 0.055 238 REMARK 3 PLANARITY : 0.012 269 REMARK 3 DIHEDRAL : 4.126 234 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 30.8114 41.4852 19.8965 REMARK 3 T TENSOR REMARK 3 T11: 0.1790 T22: 0.1372 REMARK 3 T33: 0.1407 T12: 0.0197 REMARK 3 T13: -0.0054 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.8255 L22: 2.1948 REMARK 3 L33: 0.7027 L12: 1.0316 REMARK 3 L13: 0.4210 L23: 0.9827 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: -0.0077 S13: -0.0214 REMARK 3 S21: -0.0780 S22: -0.0494 S23: 0.1132 REMARK 3 S31: 0.0857 S32: -0.0308 S33: 0.0452 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8SUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000274478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35029 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 47.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 25.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50300 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M NACL, 0.2 M MGCL2, 0.1 M TRIS, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.62400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.81200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.81200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.62400 REMARK 290 REMARK 290 REMARK: NULL 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: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 62.43600 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 580 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 6 REMARK 465 LEU A 7 REMARK 465 GLU A 8 REMARK 465 PRO A 9 REMARK 465 ASP A 206 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 10 CG OD1 OD2 REMARK 470 ARG A 26 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 39 CG CD OE1 OE2 REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 123 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 ILE A 181 CG1 CG2 CD1 REMARK 470 GLU A 182 CG CD OE1 OE2 REMARK 470 GLU A 187 CG CD OE1 OE2 REMARK 470 GLU A 191 CG CD OE1 OE2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 584 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 585 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH A 586 DISTANCE = 7.83 ANGSTROMS DBREF 8SUA A 1 206 PDB 8SUA 8SUA 1 206 SEQRES 1 A 206 MSE SER ALA SER ALA GLU LEU GLU PRO ASP VAL LYS GLY SEQRES 2 A 206 ARG ILE LEU ASP ALA ALA ALA ASP ALA PHE MSE ALA ARG SEQRES 3 A 206 GLY PHE ALA ASN THR THR ILE ASP ASP ILE ALA ASP GLU SEQRES 4 A 206 VAL GLY ALA THR LYS GLY LEU ILE TYR TYR HIS PHE ARG SEQRES 5 A 206 SER LYS PHE ASP ILE PHE LEU ALA VAL TYR GLU ASP GLY SEQRES 6 A 206 MSE ARG ARG VAL ARG GLU ARG VAL GLU PRO HIS SER THR SEQRES 7 A 206 ALA PRO GLY THR GLY HIS GLN ARG LEU GLU ALA MSE SER SEQRES 8 A 206 ILE ALA HIS LEU GLU ASN LEU MSE THR GLU LEU GLY TYR SEQRES 9 A 206 HIS HIS VAL VAL HIS GLN GLY VAL ARG HIS GLN ASP SER SEQRES 10 A 206 THR ALA LEU LYS VAL ARG GLN ARG ASP ALA LEU THR ALA SEQRES 11 A 206 LEU ASN GLU LEU ARG ARG ASP TYR GLU ARG MSE PHE ARG SEQRES 12 A 206 ARG VAL ILE ALA GLU GLY ILE ALA ASP GLY SER LEU ARG SEQRES 13 A 206 ARG VAL ASP GLU ALA LEU ALA THR ARG THR LEU LEU SER SEQRES 14 A 206 ASN LEU ASN ALA VAL ASP VAL TRP TYR ARG LYS ILE GLU SEQRES 15 A 206 GLY GLN THR GLY GLU GLU ILE ARG GLU LEU ALA SER GLN SEQRES 16 A 206 VAL VAL ASP MSE LEU ILE GLY GLY LEU ALA ASP HET MSE A 24 17 HET MSE A 66 17 HET MSE A 90 17 HET MSE A 99 17 HET MSE A 141 17 HET MSE A 199 17 HET YT9 A 301 30 HETNAM MSE SELENOMETHIONINE HETNAM YT9 3-AZANYL-3-(HYDROXYMETHYL)-1,5,7,11-TETRAOXA-6$L^{4}- HETNAM 2 YT9 BORASPIRO[5.5]UNDECAN-9-OL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 YT9 C7 H15 B N O6 1- FORMUL 3 HOH *186(H2 O) HELIX 1 AA1 ASP A 10 THR A 31 1 22 HELIX 2 AA2 THR A 32 GLY A 41 1 10 HELIX 3 AA3 THR A 43 PHE A 51 1 9 HELIX 4 AA4 SER A 53 ALA A 79 1 27 HELIX 5 AA5 THR A 82 GLU A 101 1 20 HELIX 6 AA6 GLU A 101 GLN A 115 1 15 HELIX 7 AA7 LYS A 121 ASP A 152 1 32 HELIX 8 AA8 ASP A 159 ALA A 173 1 15 HELIX 9 AA9 VAL A 174 TRP A 177 5 4 HELIX 10 AB1 THR A 185 GLY A 203 1 19 LINK C PHE A 23 N MSE A 24 1555 1555 1.32 LINK C MSE A 24 N ALA A 25 1555 1555 1.33 LINK C GLY A 65 N MSE A 66 1555 1555 1.32 LINK C MSE A 66 N ARG A 67 1555 1555 1.34 LINK C ALA A 89 N MSE A 90 1555 1555 1.34 LINK C MSE A 90 N SER A 91 1555 1555 1.33 LINK C LEU A 98 N MSE A 99 1555 1555 1.33 LINK C MSE A 99 N THR A 100 1555 1555 1.34 LINK C ARG A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N PHE A 142 1555 1555 1.33 LINK C ASP A 198 N MSE A 199 1555 1555 1.32 LINK C MSE A 199 N LEU A 200 1555 1555 1.32 CRYST1 85.437 85.437 62.436 90.00 90.00 120.00 P 32 2 1 6 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 0.011705 0.006758 0.000000 0.00000 SCALE2 0.000000 0.013515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016016 0.00000