HEADER CHAPERONE 21-AUG-25 9Q5P TITLE STRUCTURE OF THE CLPC1-N-TERMINAL DOMAIN OF M. TUBERCULOSIS COMPLEXED TITLE 2 WITH P-ARGININE BOUND TO SITE NO.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPC1; COMPND 3 CHAIN: A; COMPND 4 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,N.M.WOLF REVDAT 1 26-AUG-26 9Q5P 0 JRNL AUTH C.ABAD-ZAPATERO,K.M.RATIA,H.LEE,S.G.FRANZBLAU,G.SHETYE, JRNL AUTH 2 T.KANEKO JRNL TITL ISOLATION, STRUCTURAL CHARACTERIZATION, AND BIOLOGICAL JRNL TITL 2 ACTIVITY OF NOVEL TERPENOID NATURAL PRODUCTS ACTIVE AGAINST JRNL TITL 3 MYCOBACTERIUM 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. 1.33 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 37988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1919 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 43.3400 - 3.2100 1.00 2791 150 0.1647 0.1769 REMARK 3 2 3.2100 - 2.5500 0.95 2522 140 0.1536 0.1694 REMARK 3 3 2.5500 - 2.2300 0.98 2602 134 0.1320 0.1408 REMARK 3 4 2.2300 - 2.0300 0.99 2578 138 0.1271 0.1514 REMARK 3 5 2.0300 - 1.8800 0.99 2587 138 0.1428 0.1496 REMARK 3 6 1.8800 - 1.7700 0.99 2573 141 0.1542 0.1916 REMARK 3 7 1.7700 - 1.6800 0.99 2607 128 0.1678 0.1898 REMARK 3 8 1.6800 - 1.6100 0.98 2495 144 0.1827 0.2229 REMARK 3 9 1.6100 - 1.5500 0.98 2557 126 0.1833 0.2084 REMARK 3 10 1.5500 - 1.4900 0.99 2538 145 0.2043 0.1881 REMARK 3 11 1.4900 - 1.4500 0.99 2521 147 0.2344 0.2310 REMARK 3 12 1.4500 - 1.4000 1.00 2559 136 0.2421 0.2466 REMARK 3 13 1.4000 - 1.3700 0.99 2562 128 0.2661 0.2651 REMARK 3 14 1.3700 - 1.3300 0.99 2577 124 0.2733 0.2993 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) : 0.126 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.396 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.67 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 1176 REMARK 3 ANGLE : 1.180 1593 REMARK 3 CHIRALITY : 0.066 185 REMARK 3 PLANARITY : 0.009 207 REMARK 3 DIHEDRAL : 6.763 174 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 9Q5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000299204. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-7.4 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97936 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL 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 : 38048 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 43.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : 0.15000 REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 1.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MCSG-1 E12, 2.5 M SODIUM MALONATE PH REMARK 280 7, 1:1 RATION OF RESERVOIR CLPC1-NTD-P-ARG SAMPLE, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 289K 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 21.23500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.71500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.71500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.23500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.26000 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: 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 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 HE22 GLN A 97 O HOH A 405 1.53 REMARK 500 HH TYR A 27 O HOH A 402 1.54 REMARK 500 OE2 GLU A 57 O HOH A 401 1.81 REMARK 500 O HOH A 406 O HOH A 487 2.05 REMARK 500 O HOH A 472 O HOH A 540 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 472 O HOH A 525 4555 1.93 REMARK 500 O HOH A 407 O HOH A 448 3555 2.12 REMARK 500 O HOH A 506 O HOH A 540 4555 2.16 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 40.03 -99.25 REMARK 500 ASN A 101 60.50 -103.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 9Q5P A 1 145 UNP P9WPC9 CLPC1_MYCTU 1 145 SEQADV 9Q5P THR A 92 UNP P9WPC9 LEU 92 CONFLICT SEQRES 1 A 145 MET PHE GLU ARG PHE THR ASP ARG ALA ARG ARG VAL VAL SEQRES 2 A 145 VAL LEU ALA GLN GLU GLU ALA ARG MET LEU ASN HIS ASN SEQRES 3 A 145 TYR ILE GLY THR GLU HIS ILE LEU LEU GLY LEU ILE HIS SEQRES 4 A 145 GLU GLY GLU GLY VAL ALA ALA LYS SER LEU GLU SER LEU SEQRES 5 A 145 GLY ILE SER LEU GLU GLY VAL ARG SER GLN VAL GLU GLU SEQRES 6 A 145 ILE ILE GLY GLN GLY GLN GLN ALA PRO SER GLY HIS ILE SEQRES 7 A 145 PRO PHE THR PRO ARG ALA LYS LYS VAL LEU GLU LEU SER SEQRES 8 A 145 THR ARG GLU ALA LEU GLN LEU GLY HIS ASN TYR ILE GLY SEQRES 9 A 145 THR GLU HIS ILE LEU LEU GLY LEU ILE ARG GLU GLY GLU SEQRES 10 A 145 GLY VAL ALA ALA GLN VAL LEU VAL LYS LEU GLY ALA GLU SEQRES 11 A 145 LEU THR ARG VAL ARG GLN GLN VAL ILE GLN LEU LEU SER SEQRES 12 A 145 GLY TYR HET RPI A 301 28 HETNAM RPI PHOSPHO-ARGININE FORMUL 2 RPI C6 H15 N4 O5 P FORMUL 3 HOH *158(H2 O) HELIX 1 AA1 THR A 6 LEU A 23 1 18 HELIX 2 AA2 GLY A 29 GLY A 41 1 13 HELIX 3 AA3 GLY A 43 LEU A 52 1 10 HELIX 4 AA4 SER A 55 GLY A 68 1 14 HELIX 5 AA5 THR A 81 GLY A 99 1 19 HELIX 6 AA6 GLY A 104 GLY A 116 1 13 HELIX 7 AA7 GLY A 118 LEU A 127 1 10 HELIX 8 AA8 GLU A 130 GLY A 144 1 15 CRYST1 42.470 54.520 71.430 90.00 90.00 90.00 P 21 21 21 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 0.023546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018342 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014000 0.00000 CONECT 2322 2331 2332 2333 2334 CONECT 2323 2324 2338 2339 CONECT 2324 2323 2325 2335 2340 CONECT 2325 2324 2326 2341 2342 CONECT 2326 2325 2327 2343 2344 CONECT 2327 2326 2328 2345 2346 CONECT 2328 2327 2329 CONECT 2329 2328 2330 2331 CONECT 2330 2329 2347 CONECT 2331 2322 2329 2348 CONECT 2332 2322 CONECT 2333 2322 CONECT 2334 2322 CONECT 2335 2324 2336 2337 CONECT 2336 2335 CONECT 2337 2335 CONECT 2338 2323 CONECT 2339 2323 CONECT 2340 2324 CONECT 2341 2325 CONECT 2342 2325 CONECT 2343 2326 CONECT 2344 2326 CONECT 2345 2327 CONECT 2346 2327 CONECT 2347 2330 CONECT 2348 2331 MASTER 279 0 1 8 0 0 0 6 1299 1 27 12 END