HEADER DNA BINDING PROTEIN 13-JUN-25 9P39 TITLE STREPTOMYCES THERMOVIOLACEUS CLPC2 C-TERMINAL DOMAIN WITH BOUND TITLE 2 PHOSPHOARGININE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPC2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES THERMOVIOLACEUS; SOURCE 3 ORGANISM_TAXID: 1952; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ER2566 KEYWDS TRANSCRIPTIONAL REGULATOR, PHOSPHOARGININE SENSOR, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.R.ANDERSON,K.R.SCHMITZ REVDAT 1 10-JUN-26 9P39 0 JRNL AUTH H.R.ANDERSON,E.C.OGBONNA,P.KANDEL,K.R.SCHMITZ JRNL TITL PHOSPHOARGININE MODULATES CLPC2 OLIGOMERIZATION AND JRNL TITL 2 TRANSCRIPTIONAL REGULATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 71.2 REMARK 3 NUMBER OF REFLECTIONS : 35725 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.630 REMARK 3 FREE R VALUE TEST SET COUNT : 3053 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 39.7700 - 3.6500 1.00 3259 202 0.1536 0.1534 REMARK 3 2 3.6500 - 2.8900 1.00 3279 203 0.1659 0.1936 REMARK 3 3 2.8900 - 2.5300 1.00 3259 196 0.1602 0.1661 REMARK 3 4 2.5300 - 2.3000 1.00 3252 194 0.1546 0.2011 REMARK 3 5 2.3000 - 2.1300 1.00 3278 196 0.1548 0.1823 REMARK 3 6 2.1300 - 2.0100 1.00 3255 196 0.1621 0.1884 REMARK 3 7 2.0100 - 1.9100 1.00 3285 189 0.1601 0.1842 REMARK 3 8 1.9100 - 1.8200 1.00 3246 197 0.1755 0.2401 REMARK 3 9 1.8200 - 1.7500 0.98 3205 184 0.1743 0.2220 REMARK 3 10 1.7500 - 1.6900 0.92 3019 184 0.1816 0.2117 REMARK 3 11 1.6900 - 1.6400 0.83 2721 160 0.1851 0.2325 REMARK 3 12 1.6400 - 1.5900 0.68 2242 128 0.1834 0.2211 REMARK 3 13 1.5900 - 1.5500 0.57 1843 116 0.1902 0.2087 REMARK 3 14 1.5500 - 1.5100 0.52 1727 100 0.2144 0.2003 REMARK 3 15 1.5100 - 1.4800 0.51 1666 98 0.2187 0.2128 REMARK 3 16 1.4800 - 1.4500 0.51 1645 97 0.2220 0.2468 REMARK 3 17 1.4500 - 1.4200 0.49 1609 96 0.2312 0.2986 REMARK 3 18 1.4200 - 1.3900 0.44 1440 86 0.2297 0.2451 REMARK 3 19 1.3900 - 1.3700 0.40 1300 77 0.2366 0.2476 REMARK 3 20 1.3700 - 1.3400 0.34 1145 69 0.2326 0.1923 REMARK 3 21 1.3400 - 1.3200 0.28 914 48 0.2483 0.1935 REMARK 3 22 1.3200 - 1.3000 0.18 596 37 0.2952 0.3455 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.122 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.969 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.85 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 : 0.009 1215 REMARK 3 ANGLE : 1.087 1646 REMARK 3 CHIRALITY : 0.061 195 REMARK 3 PLANARITY : 0.008 214 REMARK 3 DIHEDRAL : 13.525 446 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 9P39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1000297023. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-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 : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38875 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 17.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 69.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5, 1 MM PARG, AND REMARK 280 2 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 16.89600 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 33.79200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.34400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.24000 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 8.44800 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: 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. (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 GLU A 84 REMARK 465 GLN A 242 REMARK 465 ALA A 243 REMARK 465 PRO A 244 REMARK 465 ALA A 245 REMARK 465 PRO A 246 REMARK 465 ARG A 247 REMARK 465 ARG A 248 REMARK 465 ASP A 249 REMARK 465 GLN A 250 REMARK 465 ALA A 251 REMARK 465 ALA A 252 REMARK 465 GLU A 253 REMARK 465 ALA A 254 REMARK 465 GLY A 255 REMARK 465 SER A 256 REMARK 465 ALA A 257 REMARK 465 GLN A 258 REMARK 465 GLU A 259 REMARK 465 PRO A 260 REMARK 465 GLY A 261 REMARK 465 GLY A 262 REMARK 465 ALA A 263 REMARK 465 ALA A 264 REMARK 465 LEU A 265 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 ASP A 165 71.53 -107.89 REMARK 500 REMARK 500 REMARK: NULL DBREF 9P39 A 84 265 PDB 9P39 9P39 84 265 SEQRES 1 A 182 GLU SER THR ASP LEU ASP PRO SER GLN GLY PHE ASN ARG SEQRES 2 A 182 TYR THR PRO ARG ALA ARG LYS VAL VAL MET ALA ALA HIS SEQRES 3 A 182 ASP ALA ALA LYS ALA ALA ARG ASN SER GLU GLY LEU PRO SEQRES 4 A 182 VAL HIS LEU VAL LEU GLY LEU LEU THR GLU PRO GLU ALA SEQRES 5 A 182 LEU ALA ALA LYS ALA ILE GLN HIS LEU GLY VAL THR LEU SEQRES 6 A 182 GLU ALA VAL ARG GLU ALA ALA THR ALA ALA LEU PRO PRO SEQRES 7 A 182 SER SER ALA ASP ALA PRO GLU LEU ILE PRO TYR GLY PRO SEQRES 8 A 182 ALA ALA LYS LYS ALA LEU GLU LEU THR PHE ARG GLU ALA SEQRES 9 A 182 LEU ARG LEU GLY HIS ASN TYR ILE GLY THR GLU HIS ILE SEQRES 10 A 182 LEU LEU ALA LEU LEU GLU GLN GLU ASN GLY GLU GLY LEU SEQRES 11 A 182 LEU SER GLY LEU GLY LEU ASP LYS ALA ARG VAL GLU GLU SEQRES 12 A 182 TYR VAL THR THR THR LEU ALA ALA LEU LEU GLU ASP SER SEQRES 13 A 182 SER SER GLN ALA PRO ALA PRO ARG ARG ASP GLN ALA ALA SEQRES 14 A 182 GLU ALA GLY SER ALA GLN GLU PRO GLY GLY ALA ALA LEU HET EDO A 301 10 HET PEG A 302 17 HET RPI A 303 28 HET EDO A 304 10 HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM RPI PHOSPHO-ARGININE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 3 PEG C4 H10 O3 FORMUL 4 RPI C6 H15 N4 O5 P FORMUL 6 HOH *118(H2 O) HELIX 1 AA1 GLY A 93 TYR A 97 5 5 HELIX 2 AA2 THR A 98 ALA A 115 1 18 HELIX 3 AA3 LEU A 121 THR A 131 1 11 HELIX 4 AA4 ALA A 135 LEU A 144 1 10 HELIX 5 AA5 THR A 147 ALA A 157 1 11 HELIX 6 AA6 GLY A 173 GLY A 191 1 19 HELIX 7 AA7 GLY A 196 ASN A 209 1 14 HELIX 8 AA8 GLY A 212 LEU A 217 1 6 HELIX 9 AA9 ASP A 220 GLU A 237 1 18 CRYST1 74.084 74.084 50.688 90.00 90.00 120.00 P 61 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 0.013498 0.007793 0.000000 0.00000 SCALE2 0.000000 0.015586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019729 0.00000 CONECT 2355 2356 2357 2359 2360 CONECT 2356 2355 2361 CONECT 2357 2355 2358 2362 2363 CONECT 2358 2357 2364 CONECT 2359 2355 CONECT 2360 2355 CONECT 2361 2356 CONECT 2362 2357 CONECT 2363 2357 CONECT 2364 2358 CONECT 2365 2366 2367 2372 2373 CONECT 2366 2365 2374 CONECT 2367 2365 2368 2375 2376 CONECT 2368 2367 2369 CONECT 2369 2368 2370 2377 2378 CONECT 2370 2369 2371 2379 2380 CONECT 2371 2370 2381 CONECT 2372 2365 CONECT 2373 2365 CONECT 2374 2366 CONECT 2375 2367 CONECT 2376 2367 CONECT 2377 2369 CONECT 2378 2369 CONECT 2379 2370 CONECT 2380 2370 CONECT 2381 2371 CONECT 2382 2391 2392 2393 2394 CONECT 2383 2384 2398 2399 CONECT 2384 2383 2385 2395 2400 CONECT 2385 2384 2386 2401 2402 CONECT 2386 2385 2387 2403 2404 CONECT 2387 2386 2388 2405 2406 CONECT 2388 2387 2389 2407 CONECT 2389 2388 2390 2391 CONECT 2390 2389 2408 CONECT 2391 2382 2389 2409 CONECT 2392 2382 CONECT 2393 2382 CONECT 2394 2382 CONECT 2395 2384 2396 2397 CONECT 2396 2395 CONECT 2397 2395 CONECT 2398 2383 CONECT 2399 2383 CONECT 2400 2384 CONECT 2401 2385 CONECT 2402 2385 CONECT 2403 2386 CONECT 2404 2386 CONECT 2405 2387 CONECT 2406 2387 CONECT 2407 2388 CONECT 2408 2390 CONECT 2409 2391 CONECT 2410 2411 2412 2414 2415 CONECT 2411 2410 2416 CONECT 2412 2410 2413 2417 2418 CONECT 2413 2412 2419 CONECT 2414 2410 CONECT 2415 2410 CONECT 2416 2411 CONECT 2417 2412 CONECT 2418 2412 CONECT 2419 2413 MASTER 269 0 4 9 0 0 0 6 1318 1 65 14 END