HEADER SIGNALING PROTEIN 07-JUL-22 8AD6 TITLE STRUCTURE OF DARB BOUND TO C-DI-AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CBS DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: B4417_3749, BATEQ7PJ16_1575, C6Y43_13715, FAL52_03995; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS C-DI-AMP, POTASSIUM STRESS, PPGPP, REL, STRINGENT FACTOR, CBPB, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GARCIA-PINO,A.TALAVERA REVDAT 2 07-FEB-24 8AD6 1 REMARK REVDAT 1 19-JUL-23 8AD6 0 JRNL AUTH A.GARCIA-PINO,A.TALAVERA JRNL TITL STRUCTURE OF DARB BOUND TO C-DI-AMP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 40317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.73 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 2332 REMARK 3 ANGLE : 0.922 3185 REMARK 3 CHIRALITY : 0.064 377 REMARK 3 PLANARITY : 0.006 451 REMARK 3 DIHEDRAL : 16.773 918 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8AD6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124196. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40317 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 52.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6YJ8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE 0.1 M MES 6.0 20 REMARK 280 % W/V PEG 4000, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.16K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 52.80850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.48700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.14650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.48700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.80850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.14650 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: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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. (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 MET A 1 REMARK 465 ILE A 2 REMARK 465 SER A 3 REMARK 465 LEU A 145 REMARK 465 ASN A 146 REMARK 465 LYS A 147 REMARK 465 MET B 1 REMARK 465 ILE B 2 REMARK 465 SER B 3 REMARK 465 LEU B 4 REMARK 465 GLN B 5 REMARK 465 SER B 6 REMARK 465 ASP B 7 REMARK 465 GLN B 8 REMARK 465 LEU B 9 REMARK 465 SER B 144 REMARK 465 LEU B 145 REMARK 465 ASN B 146 REMARK 465 LYS B 147 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 LEU A 10 CG CD1 CD2 REMARK 470 ILE A 142 CG1 CG2 CD1 REMARK 470 SER A 144 OG REMARK 470 GLU B 11 CG CD OE1 OE2 REMARK 470 ARG B 96 CD NE CZ NH1 NH2 REMARK 470 ASP B 121 CG OD1 OD2 REMARK 470 GLU B 122 CG CD OE1 OE2 REMARK 470 ARG B 143 CZ NH1 NH2 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 TYR A 55 30.22 72.93 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8AD6 A 1 147 UNP A0A164SLA6_BACIU DBREF2 8AD6 A A0A164SLA6 1 147 DBREF1 8AD6 B 1 147 UNP A0A164SLA6_BACIU DBREF2 8AD6 B A0A164SLA6 1 147 SEQRES 1 A 147 MET ILE SER LEU GLN SER ASP GLN LEU LEU GLU ALA THR SEQRES 2 A 147 VAL GLY GLN PHE MET ILE GLU ALA ASP LYS VAL ALA HIS SEQRES 3 A 147 VAL GLN VAL GLY ASN ASN LEU GLU HIS ALA LEU LEU VAL SEQRES 4 A 147 LEU THR LYS THR GLY TYR THR ALA ILE PRO VAL LEU ASP SEQRES 5 A 147 PRO SER TYR ARG LEU HIS GLY LEU ILE GLY THR ASN MET SEQRES 6 A 147 ILE MET ASN SER ILE PHE GLY LEU GLU ARG ILE GLU PHE SEQRES 7 A 147 GLU LYS LEU ASP GLN ILE THR VAL GLU GLU VAL MET LEU SEQRES 8 A 147 THR ASP ILE PRO ARG LEU HIS ILE ASN ASP PRO ILE MET SEQRES 9 A 147 LYS GLY PHE GLY MET VAL ILE ASN ASN GLY PHE VAL CYS SEQRES 10 A 147 VAL GLU ASN ASP GLU GLN VAL PHE GLU GLY ILE PHE THR SEQRES 11 A 147 ARG ARG VAL VAL LEU LYS GLU LEU ASN LYS HIS ILE ARG SEQRES 12 A 147 SER LEU ASN LYS SEQRES 1 B 147 MET ILE SER LEU GLN SER ASP GLN LEU LEU GLU ALA THR SEQRES 2 B 147 VAL GLY GLN PHE MET ILE GLU ALA ASP LYS VAL ALA HIS SEQRES 3 B 147 VAL GLN VAL GLY ASN ASN LEU GLU HIS ALA LEU LEU VAL SEQRES 4 B 147 LEU THR LYS THR GLY TYR THR ALA ILE PRO VAL LEU ASP SEQRES 5 B 147 PRO SER TYR ARG LEU HIS GLY LEU ILE GLY THR ASN MET SEQRES 6 B 147 ILE MET ASN SER ILE PHE GLY LEU GLU ARG ILE GLU PHE SEQRES 7 B 147 GLU LYS LEU ASP GLN ILE THR VAL GLU GLU VAL MET LEU SEQRES 8 B 147 THR ASP ILE PRO ARG LEU HIS ILE ASN ASP PRO ILE MET SEQRES 9 B 147 LYS GLY PHE GLY MET VAL ILE ASN ASN GLY PHE VAL CYS SEQRES 10 B 147 VAL GLU ASN ASP GLU GLN VAL PHE GLU GLY ILE PHE THR SEQRES 11 B 147 ARG ARG VAL VAL LEU LYS GLU LEU ASN LYS HIS ILE ARG SEQRES 12 B 147 SER LEU ASN LYS HET 2BA A 201 44 HET 2BA B 201 44 HETNAM 2BA (2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6- HETNAM 2 2BA AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3', HETNAM 3 2BA 2'-J][1,3,7,9,2,8 ]TETRAOXADIPHOSPHACYCLODODECINE-3,5, HETNAM 4 2BA 10,12-TETROL 5,12-DIOXIDE HETSYN 2BA BIS-(3',5')-CYCLIC-DIMERIC-ADENOSINE-MONOPHOSPHATE FORMUL 3 2BA 2(C20 H24 N10 O12 P2) FORMUL 5 HOH *271(H2 O) HELIX 1 AA1 GLN A 5 LEU A 10 1 6 HELIX 2 AA2 THR A 13 PHE A 17 5 5 HELIX 3 AA3 ASP A 22 VAL A 24 5 3 HELIX 4 AA4 ASN A 32 GLY A 44 1 13 HELIX 5 AA5 THR A 63 PHE A 71 1 9 HELIX 6 AA6 GLU A 77 GLN A 83 5 7 HELIX 7 AA7 THR A 85 MET A 90 1 6 HELIX 8 AA8 PRO A 102 VAL A 110 1 9 HELIX 9 AA9 ARG A 131 SER A 144 1 14 HELIX 10 AB1 THR B 13 MET B 18 1 6 HELIX 11 AB2 ASP B 22 VAL B 24 5 3 HELIX 12 AB3 ASN B 32 GLY B 44 1 13 HELIX 13 AB4 THR B 63 PHE B 71 1 9 HELIX 14 AB5 GLU B 77 LEU B 81 5 5 HELIX 15 AB6 THR B 85 VAL B 89 5 5 HELIX 16 AB7 PRO B 102 VAL B 110 1 9 HELIX 17 AB8 ARG B 131 ARG B 143 1 13 SHEET 1 AA1 4 ILE A 19 GLU A 20 0 SHEET 2 AA1 4 PHE A 125 THR A 130 -1 O ILE A 128 N ILE A 19 SHEET 3 AA1 4 PHE A 115 GLU A 119 -1 N VAL A 118 O GLU A 126 SHEET 4 AA1 4 ARG A 96 HIS A 98 1 N LEU A 97 O GLU A 119 SHEET 1 AA2 3 VAL A 27 GLN A 28 0 SHEET 2 AA2 3 ALA A 47 LEU A 51 1 O LEU A 51 N VAL A 27 SHEET 3 AA2 3 LEU A 57 GLY A 62 -1 O HIS A 58 N VAL A 50 SHEET 1 AA3 4 ILE B 19 GLU B 20 0 SHEET 2 AA3 4 PHE B 125 THR B 130 -1 O ILE B 128 N ILE B 19 SHEET 3 AA3 4 PHE B 115 GLU B 119 -1 N VAL B 118 O GLU B 126 SHEET 4 AA3 4 ARG B 96 LEU B 97 1 N LEU B 97 O GLU B 119 SHEET 1 AA4 3 VAL B 27 GLN B 28 0 SHEET 2 AA4 3 ALA B 47 LEU B 51 1 O LEU B 51 N VAL B 27 SHEET 3 AA4 3 LEU B 57 GLY B 62 -1 O HIS B 58 N VAL B 50 CRYST1 105.617 42.293 64.974 90.00 90.00 90.00 P 21 21 21 8 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 0.009468 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023645 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015391 0.00000