HEADER CYTOSOLIC PROTEIN 06-OCT-22 8B9O TITLE STRUCTURE OF THE C-TERMINAL DOMAIN OF CLPC2 FROM MYCOBACTERIUM TITLE 2 SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLP AMINO TERMINAL DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 1772; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 GENE: MSMEG_2792; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRESS RESISTANCE PROTEIN, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.MEINHART,D.M.HOI,T.CLAUSEN REVDAT 3 07-FEB-24 8B9O 1 REMARK REVDAT 2 12-JUL-23 8B9O 1 JRNL REVDAT 1 05-JUL-23 8B9O 0 JRNL AUTH D.M.HOI,S.JUNKER,L.JUNK,K.SCHWECHEL,K.FISCHEL, JRNL AUTH 2 D.PODLESAINSKI,P.M.E.HAWKINS,L.VAN GEELEN,F.KASCHANI, JRNL AUTH 3 J.LEODOLTER,F.E.MORREALE,S.KLEINE,S.GUHA,K.RUMPEL, JRNL AUTH 4 V.M.SCHMIEDEL,H.WEINSTABL,A.MEINHART,R.J.PAYNE,M.KAISER, JRNL AUTH 5 M.HARTL,G.BOEHMELT,U.KAZMAIER,R.KALSCHEUER,T.CLAUSEN JRNL TITL CLP-TARGETING BACPROTACS IMPAIR MYCOBACTERIAL PROTEOSTASIS JRNL TITL 2 AND SURVIVAL. JRNL REF CELL V. 186 2176 2023 JRNL REFN ISSN 1097-4172 JRNL PMID 37137307 JRNL DOI 10.1016/J.CELL.2023.04.009 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20_4459: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 8936 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 446 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 32.2000 - 2.8900 0.99 2886 152 0.1814 0.1970 REMARK 3 2 2.8900 - 2.2900 1.00 2847 150 0.2695 0.3179 REMARK 3 3 2.2900 - 2.0000 0.97 2757 144 0.2834 0.3284 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.850 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 : 0.004 NULL REMARK 3 ANGLE : 0.611 NULL REMARK 3 CHIRALITY : 0.041 178 REMARK 3 PLANARITY : 0.006 199 REMARK 3 DIHEDRAL : 6.702 157 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 199 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7560 -12.9748 13.2939 REMARK 3 T TENSOR REMARK 3 T11: 0.4229 T22: 0.4742 REMARK 3 T33: 0.5421 T12: -0.0860 REMARK 3 T13: -0.0420 T23: -0.0541 REMARK 3 L TENSOR REMARK 3 L11: 1.8434 L22: 5.2986 REMARK 3 L33: 6.5415 L12: 1.5085 REMARK 3 L13: -1.3518 L23: -1.7620 REMARK 3 S TENSOR REMARK 3 S11: -0.2236 S12: 0.5569 S13: -0.4289 REMARK 3 S21: -0.4090 S22: 0.7330 S23: 0.5738 REMARK 3 S31: 0.3939 S32: -1.0801 S33: -0.4545 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 200 THROUGH 240 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2059 -17.4257 18.1106 REMARK 3 T TENSOR REMARK 3 T11: 0.5343 T22: 0.4490 REMARK 3 T33: 0.5048 T12: 0.0870 REMARK 3 T13: -0.0149 T23: -0.1428 REMARK 3 L TENSOR REMARK 3 L11: 5.7111 L22: 6.8208 REMARK 3 L33: 7.4124 L12: 1.5744 REMARK 3 L13: 3.6245 L23: -0.9296 REMARK 3 S TENSOR REMARK 3 S11: 0.0951 S12: 0.5907 S13: -0.6113 REMARK 3 S21: -0.2390 S22: -0.0174 S23: -0.7628 REMARK 3 S31: 1.3586 S32: 0.0835 S33: 0.0006 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 135 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5822 0.0050 14.1542 REMARK 3 T TENSOR REMARK 3 T11: 0.3262 T22: 0.3324 REMARK 3 T33: 0.3106 T12: 0.0402 REMARK 3 T13: 0.0451 T23: -0.1007 REMARK 3 L TENSOR REMARK 3 L11: 4.1640 L22: 8.2091 REMARK 3 L33: 9.9429 L12: -0.2818 REMARK 3 L13: 0.6876 L23: -1.1000 REMARK 3 S TENSOR REMARK 3 S11: 0.2950 S12: 0.5244 S13: -0.0061 REMARK 3 S21: -0.1717 S22: 0.0004 S23: -0.1957 REMARK 3 S31: -0.5670 S32: 0.0181 S33: -0.2332 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 136 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4130 -4.5145 15.4362 REMARK 3 T TENSOR REMARK 3 T11: 0.4242 T22: 0.4329 REMARK 3 T33: 0.4254 T12: 0.0129 REMARK 3 T13: -0.0567 T23: -0.1022 REMARK 3 L TENSOR REMARK 3 L11: 3.8266 L22: 3.4537 REMARK 3 L33: 3.2910 L12: 1.1795 REMARK 3 L13: -1.0963 L23: -1.5143 REMARK 3 S TENSOR REMARK 3 S11: -0.1069 S12: 0.1450 S13: -0.2850 REMARK 3 S21: 0.3259 S22: -0.2468 S23: -0.7735 REMARK 3 S31: -0.4231 S32: 0.5100 S33: 0.3185 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 8B9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8941 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 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: 3WDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% (W/V) PEG 1000, 12.5% (W/V) PEG REMARK 280 3350, 12.5% (V/V) MPD, 0.02 M OF EACH AMINO ACID AND 0.1 M MES/ REMARK 280 IMIDAZOLE PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 25.54000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.31500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.54000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.31500 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 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 MET A 98 REMARK 465 GLU A 168 REMARK 465 ALA A 169 REMARK 465 LYS A 241 REMARK 465 PRO A 242 REMARK 465 ALA A 243 REMARK 465 GLU A 244 REMARK 465 LEU A 245 REMARK 465 GLU A 246 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 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 ALA A 171 -59.89 61.57 REMARK 500 ASP A 214 40.79 -104.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 RPI A 301 DBREF 8B9O A 99 240 UNP A0QW35 A0QW35_MYCS2 99 240 SEQADV 8B9O MET A 98 UNP A0QW35 INITIATING METHIONINE SEQADV 8B9O LYS A 241 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O PRO A 242 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O ALA A 243 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O GLU A 244 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O LEU A 245 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O GLU A 246 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O HIS A 247 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O HIS A 248 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O HIS A 249 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O HIS A 250 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O HIS A 251 UNP A0QW35 EXPRESSION TAG SEQADV 8B9O HIS A 252 UNP A0QW35 EXPRESSION TAG SEQRES 1 A 155 MET PHE GLY ARG PHE THR PRO ARG ALA ARG ASN VAL ILE SEQRES 2 A 155 VAL VAL ALA HIS ASN LEU ALA HIS ASP ALA ARG ASN ALA SEQRES 3 A 155 GLU ILE THR PRO ASP HIS LEU LEU LEU GLY LEU PHE ALA SEQRES 4 A 155 ASP THR GLU GLY LEU ALA ALA LYS LEU LEU ALA GLY GLN SEQRES 5 A 155 GLY VAL ASP ALA ASP ALA VAL ARG ALA ALA VAL THR LEU SEQRES 6 A 155 PRO PRO SER THR GLY GLU ALA ALA ALA LEU ILE PRO PHE SEQRES 7 A 155 ASP THR ALA ALA LYS LYS ALA LEU GLU LEU THR PHE ARG SEQRES 8 A 155 GLN ALA LEU ARG LEU GLY HIS ASN TYR ILE GLY THR GLU SEQRES 9 A 155 HIS ILE LEU LEU ALA LEU VAL ASP ALA GLU ASP GLY ASP SEQRES 10 A 155 GLY PRO LEU HIS ARG LEU GLY VAL ASP ALA GLU ARG PHE SEQRES 11 A 155 GLU ALA ASP LEU ARG THR ALA LEU GLU PRO PHE MET THR SEQRES 12 A 155 LYS PRO ALA GLU LEU GLU HIS HIS HIS HIS HIS HIS HET RPI A 301 15 HETNAM RPI PHOSPHO-ARGININE FORMUL 2 RPI C6 H15 N4 O5 P FORMUL 3 HOH *6(H2 O) HELIX 1 AA1 THR A 103 ARG A 121 1 19 HELIX 2 AA2 THR A 126 PHE A 135 1 10 HELIX 3 AA3 GLY A 140 GLN A 149 1 10 HELIX 4 AA4 ASP A 152 ALA A 159 1 8 HELIX 5 AA5 ASP A 176 GLY A 194 1 19 HELIX 6 AA6 GLY A 199 ALA A 210 1 12 HELIX 7 AA7 GLY A 215 LEU A 220 1 6 HELIX 8 AA8 ASP A 223 GLU A 236 1 14 CRYST1 51.080 40.630 64.430 90.00 91.75 90.00 C 1 2 1 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 0.019577 0.000000 0.000598 0.00000 SCALE2 0.000000 0.024612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015528 0.00000