HEADER TRANSCRIPTION 14-JUN-23 8T5Y TITLE STRUCTURE OF RHODOCOCCUS SP. USK13 DARR(K44A)-CAMP 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: RHODOCOCCUS SP. USK13; SOURCE 3 ORGANISM_TAXID: 2806442; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAMP, DARR, MYCOBACTERIA, TETR, TFR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 2 22-NOV-23 8T5Y 1 JRNL REVDAT 1 01-NOV-23 8T5Y 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. 1.44 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 42881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 49.2000 - 3.4700 1.00 3129 154 0.1679 0.1683 REMARK 3 2 3.4700 - 2.7500 1.00 2982 145 0.1779 0.1737 REMARK 3 3 2.7500 - 2.4100 1.00 2945 144 0.1805 0.2063 REMARK 3 4 2.4100 - 2.1900 1.00 2929 144 0.1833 0.1959 REMARK 3 5 2.1900 - 2.0300 1.00 2913 142 0.1909 0.1938 REMARK 3 6 2.0300 - 1.9100 1.00 2904 142 0.2089 0.2293 REMARK 3 7 1.9100 - 1.8100 1.00 2894 142 0.2119 0.2475 REMARK 3 8 1.8100 - 1.7400 1.00 2902 141 0.2026 0.2239 REMARK 3 9 1.7400 - 1.6700 1.00 2892 142 0.2265 0.2765 REMARK 3 10 1.6700 - 1.6100 1.00 2889 142 0.2383 0.2955 REMARK 3 11 1.6100 - 1.5600 1.00 2878 140 0.2040 0.2098 REMARK 3 12 1.5600 - 1.5200 1.00 2856 140 0.2102 0.2361 REMARK 3 13 1.5200 - 1.4800 1.00 2883 141 0.2238 0.2531 REMARK 3 14 1.4800 - 1.4400 1.00 2885 141 0.2404 0.2591 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) : 19.040 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 : 0.006 NULL REMARK 3 ANGLE : 0.892 NULL REMARK 3 CHIRALITY : 0.064 254 REMARK 3 PLANARITY : 0.008 294 REMARK 3 DIHEDRAL : 9.578 245 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): 14.6438 9.9586 20.3370 REMARK 3 T TENSOR REMARK 3 T11: 0.1255 T22: 0.1248 REMARK 3 T33: 0.1948 T12: -0.0044 REMARK 3 T13: -0.0059 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.4027 L22: 0.7800 REMARK 3 L33: 3.0386 L12: -0.2698 REMARK 3 L13: -0.2598 L23: 0.8394 REMARK 3 S TENSOR REMARK 3 S11: 0.0295 S12: -0.0277 S13: 0.0273 REMARK 3 S21: -0.0160 S22: -0.0350 S23: 0.0360 REMARK 3 S31: -0.0809 S32: -0.0063 S33: 0.0035 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 8T5Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-23 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 : 5.0.1 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 543824 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 49.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 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) : 0.98800 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 800 MM SUCCINIC ACID PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 22.70450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.70450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.25500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 -1.000000 0.000000 0.000000 45.40900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 614 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 768 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 841 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 GLY A 111 REMARK 465 VAL A 112 REMARK 465 ALA A 208 REMARK 465 ASP A 209 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 SER A 9 OG REMARK 470 GLN A 110 CG CD OE1 NE2 REMARK 470 ASP A 114 CG OD1 OD2 REMARK 470 THR A 118 OG1 CG2 REMARK 470 GLU A 182 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 853 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 854 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 855 DISTANCE = 6.25 ANGSTROMS DBREF 8T5Y A -2 209 PDB 8T5Y 8T5Y -2 209 SEQRES 1 A 212 GLY SER HIS MET SER ALA SER ALA GLU PRO GLU SER ASP SEQRES 2 A 212 VAL LYS GLY ARG ILE LEU ASP ALA ALA ALA ASP ALA PHE SEQRES 3 A 212 MET LEU ARG GLY PHE ALA ASN THR THR ILE ASP ASP ILE SEQRES 4 A 212 ALA ASP ASP VAL GLY ALA THR ALA GLY LEU ILE TYR TYR SEQRES 5 A 212 HIS PHE ARG SER LYS PHE ASP ILE PHE LEU ALA VAL TYR SEQRES 6 A 212 GLU ASP GLY MET ARG ARG VAL ARG GLU ARG VAL GLU PRO SEQRES 7 A 212 TYR VAL GLY ALA PRO GLY THR GLY ARG GLN ARG LEU VAL SEQRES 8 A 212 ALA MET SER VAL ALA HIS VAL GLU ASN LEU MET ILE ASP SEQRES 9 A 212 LEU GLY TYR HIS HIS VAL VAL HIS GLN GLY VAL ARG ASP SEQRES 10 A 212 GLN ALA SER THR ALA LEU LYS VAL ARG GLN ARG ASP ALA SEQRES 11 A 212 LEU ALA ALA LEU ASN GLU LEU ARG ARG ASP TYR GLU ARG SEQRES 12 A 212 MET PHE HIS HIS VAL ILE THR GLU GLY ILE ALA ASP GLY SEQRES 13 A 212 SER LEU ARG ASN VAL ASP ASP ALA LEU ALA THR ARG THR SEQRES 14 A 212 LEU LEU SER ASN LEU ASN ALA VAL ASP VAL TRP TYR ARG SEQRES 15 A 212 LYS ILE GLU GLY GLN THR GLU LYS GLU VAL HIS ASP LEU SEQRES 16 A 212 ALA SER GLN VAL VAL ASP LEU LEU ILE GLY GLY ILE GLY SEQRES 17 A 212 ALA THR ALA ASP HET CMP A 501 22 HETNAM CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE HETSYN CMP CYCLIC AMP; CAMP FORMUL 2 CMP C10 H12 N5 O6 P FORMUL 3 HOH *255(H2 O) HELIX 1 AA1 PRO A 7 GLY A 27 1 21 HELIX 2 AA2 THR A 32 VAL A 40 1 9 HELIX 3 AA3 THR A 43 PHE A 51 1 9 HELIX 4 AA4 SER A 53 GLU A 74 1 22 HELIX 5 AA5 PRO A 75 VAL A 77 5 3 HELIX 6 AA6 THR A 82 ASP A 101 1 20 HELIX 7 AA7 ASP A 101 GLN A 110 1 10 HELIX 8 AA8 LYS A 121 ASP A 152 1 32 HELIX 9 AA9 ASP A 159 ALA A 173 1 15 HELIX 10 AB1 VAL A 174 TRP A 177 5 4 HELIX 11 AB2 THR A 185 GLY A 203 1 19 CRYST1 45.409 60.510 84.520 90.00 90.00 90.00 P 21 21 2 4 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 0.022022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011832 0.00000