HEADER CHAPERONE 19-AUG-25 9Q3Z TITLE STRUCTURE OF THE CLPC1-N-TERMINAL DOMAIN OF M. TUBERCULOSIS COMPLEXED TITLE 2 WITH P-ARGININE BOUND TO SITE NO. 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPC1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: CLPC1, RV3596C, MTCY07H7B.26; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CLPC1 ATPASE, RUFOMYCIN, ANTIBIOTIC, CLPC1-NTD-COMPLEX, CHAPERONE, KEYWDS 2 CHAPERONE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.ABAD-ZAPATERO,K.M.RATIA REVDAT 1 19-AUG-26 9Q3Z 0 JRNL AUTH C.ABAD-ZAPATERO,K.M.RATIA,H.LEE,T.KANEKO,S.G.FRANZBLAU, JRNL AUTH 2 G.SHETYE JRNL TITL ISOLATION, STRUCTURAL CHARACTERIZATION AND BIOLOGICAL JRNL TITL 2 ACTIVITY OF RYUKYULACTONES, NOVEL TERPENE ANALOGS FROM JRNL TITL 3 MICROMONOSPORA SP AND ACTINOMADURA SP ACTIVE AGAINST M. JRNL TITL 4 TUBERCULOSIS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.M.WOLF,H.LEE,M.P.CHOULES,G.F.PAULI,R.PHANSALKAR, REMARK 1 AUTH 2 J.R.ANDERSON,W.GAO,J.REN,B.D.SANTARSIERO,H.LEE,J.CHENG, REMARK 1 AUTH 3 Y.Y.JIN,N.A.HO,N.M.DUC,J.W.SUH,C.ABAD-ZAPATERO,S.CHO REMARK 1 TITL HIGH-RESOLUTION STRUCTURE OF CLPC1-RUFOMYCIN AND LIGAND REMARK 1 TITL 2 BINDING STUDIES PROVIDE A FRAMEWORK TO DESIGN AND OPTIMIZE REMARK 1 TITL 3 ANTI-TUBERCULOSIS LEADS. REMARK 1 REF ACS INFECT DIS. V. 5 829 2019 REMARK 1 REFN ESSN 2373-8227 REMARK 1 PMID 30990022 REMARK 1 DOI 10.1021/ACSINFECDIS.8B00276 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.ZHOU,G.SHETYE,L.L.KLEIN,N.M.WOLF,H.LEE,J.B.MCALPINE, REMARK 1 AUTH 2 G.HARRIS,S.N.CHEN,J.W.SUH,S.H.CHO,S.G.FRANZBLAU, REMARK 1 AUTH 3 C.ABAD-ZAPATERO,G.F.PAULI REMARK 1 TITL STRUCTURE-BASED ANALYSIS OF SEMISYNTHETIC ANTI-TB RUFOMYCIN REMARK 1 TITL 2 ANALOGUES. REMARK 1 REF J.NAT.PROD. V. 88 907 2025 REMARK 1 REFN ESSN 1520-6025 REMARK 1 PMID 40126472 REMARK 1 DOI 10.1021/ACS.JNATPROD.4C01266 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 20290 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1115 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 33.0600 - 3.0500 0.99 2430 155 0.1600 0.1672 REMARK 3 2 3.0500 - 2.4200 1.00 2415 138 0.1579 0.1949 REMARK 3 3 2.4200 - 2.1200 0.99 2421 141 0.1488 0.1843 REMARK 3 4 2.1200 - 1.9200 0.99 2400 134 0.1566 0.2062 REMARK 3 5 1.9200 - 1.7800 0.98 2401 144 0.1574 0.1960 REMARK 3 6 1.7800 - 1.6800 0.98 2371 150 0.1615 0.2145 REMARK 3 7 1.6800 - 1.6000 0.98 2379 136 0.1728 0.1966 REMARK 3 8 1.6000 - 1.5300 0.97 2358 117 0.1795 0.2165 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.93 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 : 0.008 1203 REMARK 3 ANGLE : 1.069 1620 REMARK 3 CHIRALITY : 0.054 188 REMARK 3 PLANARITY : 0.016 209 REMARK 3 DIHEDRAL : 7.141 170 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 9Q3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000299163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : DIAMOND REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 60.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.19700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.5, 25% PEG 3350, REMARK 280 1:1 RATIO OF RESERVOIR TO DROP, 2 MM P-ARG, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.16500 REMARK 290 SMTRY3 2 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: 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 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH12 ARG A 11 O HOH A 304 1.51 REMARK 500 O HOH A 373 O HOH A 400 2.10 REMARK 500 O HOH A 427 O HOH A 442 2.14 REMARK 500 OE1 GLU A 64 O HOH A 301 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 26 40.37 -105.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 11 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9Q3Z A 1 145 UNP P9WPC9 CLPC1_MYCTU 1 145 SEQADV 9Q3Z LYS A 146 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z LEU A 147 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z ALA A 148 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z ALA A 149 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z ALA A 150 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z LEU A 151 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z GLU A 152 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z HIS A 153 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z HIS A 154 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z HIS A 155 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z HIS A 156 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z HIS A 157 UNP P9WPC9 EXPRESSION TAG SEQADV 9Q3Z HIS A 158 UNP P9WPC9 EXPRESSION TAG SEQRES 1 A 158 MET PHE GLU ARG PHE THR ASP ARG ALA ARG ARG VAL VAL SEQRES 2 A 158 VAL LEU ALA GLN GLU GLU ALA ARG MET LEU ASN HIS ASN SEQRES 3 A 158 TYR ILE GLY THR GLU HIS ILE LEU LEU GLY LEU ILE HIS SEQRES 4 A 158 GLU GLY GLU GLY VAL ALA ALA LYS SER LEU GLU SER LEU SEQRES 5 A 158 GLY ILE SER LEU GLU GLY VAL ARG SER GLN VAL GLU GLU SEQRES 6 A 158 ILE ILE GLY GLN GLY GLN GLN ALA PRO SER GLY HIS ILE SEQRES 7 A 158 PRO PHE THR PRO ARG ALA LYS LYS VAL LEU GLU LEU SER SEQRES 8 A 158 LEU ARG GLU ALA LEU GLN LEU GLY HIS ASN TYR ILE GLY SEQRES 9 A 158 THR GLU HIS ILE LEU LEU GLY LEU ILE ARG GLU GLY GLU SEQRES 10 A 158 GLY VAL ALA ALA GLN VAL LEU VAL LYS LEU GLY ALA GLU SEQRES 11 A 158 LEU THR ARG VAL ARG GLN GLN VAL ILE GLN LEU LEU SER SEQRES 12 A 158 GLY TYR LYS LEU ALA ALA ALA LEU GLU HIS HIS HIS HIS SEQRES 13 A 158 HIS HIS HET RPI A 201 28 HETNAM RPI PHOSPHO-ARGININE FORMUL 2 RPI C6 H15 N4 O5 P FORMUL 3 HOH *144(H2 O) HELIX 1 AA1 MET A 1 PHE A 5 5 5 HELIX 2 AA2 THR A 6 LEU A 23 1 18 HELIX 3 AA3 GLY A 29 GLY A 41 1 13 HELIX 4 AA4 GLY A 43 LEU A 52 1 10 HELIX 5 AA5 SER A 55 ILE A 67 1 13 HELIX 6 AA6 THR A 81 LEU A 98 1 18 HELIX 7 AA7 GLY A 104 GLY A 116 1 13 HELIX 8 AA8 GLY A 118 LEU A 127 1 10 HELIX 9 AA9 GLU A 130 GLU A 152 1 23 CRYST1 34.370 60.330 36.140 90.00 113.81 90.00 P 1 21 1 2 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 0.029095 0.000000 0.012839 0.00000 SCALE2 0.000000 0.016576 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030244 0.00000 CONECT 2389 2398 2399 2400 2401 CONECT 2390 2391 2405 2406 CONECT 2391 2390 2392 2402 2407 CONECT 2392 2391 2393 2408 2409 CONECT 2393 2392 2394 2410 2411 CONECT 2394 2393 2395 2412 2413 CONECT 2395 2394 2396 CONECT 2396 2395 2397 2398 CONECT 2397 2396 2414 CONECT 2398 2389 2396 2415 CONECT 2399 2389 CONECT 2400 2389 CONECT 2401 2389 CONECT 2402 2391 2403 2404 CONECT 2403 2402 CONECT 2404 2402 CONECT 2405 2390 CONECT 2406 2390 CONECT 2407 2391 CONECT 2408 2392 CONECT 2409 2392 CONECT 2410 2393 CONECT 2411 2393 CONECT 2412 2394 CONECT 2413 2394 CONECT 2414 2397 CONECT 2415 2398 MASTER 271 0 1 9 0 0 0 6 1334 1 27 13 END