HEADER CHAPERONE 06-JAN-22 7TFM TITLE ATOMIC STRUCTURE OF THE LEISHMANIA SPP. HSP100 N-DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE SUBUNIT, HEAT SHOCK PROTEIN 100 COMPND 3 (HSP100); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MEXICANA MHOM/GT/2001/U1103; SOURCE 3 ORGANISM_TAXID: 929439; SOURCE 4 STRAIN: MHOM/GT/2001/U1103; SOURCE 5 GENE: LMXM_08_29_1270; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: CODONPLUS (DE3)-RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPROEX-HTB KEYWDS MOLECULAR CHAPERONE, PROTEIN UNFOLDASE, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MERCADO,S.LEE,C.CHANG,N.SUNG,L.SOONG,A.CATIC,F.T.F.TSAI REVDAT 3 18-OCT-23 7TFM 1 REMARK REVDAT 2 27-APR-22 7TFM 1 JRNL REVDAT 1 16-FEB-22 7TFM 0 JRNL AUTH J.M.MERCADO,S.LEE,C.CHANG,N.SUNG,L.SOONG,A.CATIC,F.T.F.TSAI JRNL TITL ATOMIC STRUCTURE OF THE LEISHMANIA SPP. HSP100 N-DOMAIN. JRNL REF PROTEINS V. 90 1242 2022 JRNL REFN ESSN 1097-0134 JRNL PMID 35122310 JRNL DOI 10.1002/PROT.26310 REMARK 2 REMARK 2 RESOLUTION. 1.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 60.9 REMARK 3 NUMBER OF REFLECTIONS : 41615 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.470 REMARK 3 FREE R VALUE TEST SET COUNT : 2515 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 36.9630 - 2.7643 0.90 5769 206 0.1419 0.1640 REMARK 3 2 2.7643 - 2.1942 0.92 5859 205 0.1415 0.1466 REMARK 3 3 2.1942 - 1.9168 0.95 6047 223 0.1280 0.1366 REMARK 3 4 1.9168 - 1.7416 0.96 6095 221 0.1293 0.1815 REMARK 3 5 1.7416 - 1.6168 0.94 6055 213 0.1238 0.1343 REMARK 3 6 1.6168 - 1.5214 0.96 6113 222 0.1181 0.1384 REMARK 3 7 1.5214 - 1.4452 0.97 6193 226 0.1181 0.1407 REMARK 3 8 1.4452 - 1.3823 0.97 6186 223 0.1232 0.1557 REMARK 3 9 1.3823 - 1.3291 0.92 5882 214 0.1265 0.1623 REMARK 3 10 1.3291 - 1.2832 0.86 5529 185 0.1288 0.1335 REMARK 3 11 1.2832 - 1.2431 0.69 4370 155 0.1223 0.1429 REMARK 3 12 1.2431 - 1.2076 0.43 2767 105 0.1138 0.1432 REMARK 3 13 1.2076 - 1.1758 0.27 1707 69 0.1187 0.1435 REMARK 3 14 1.1758 - 1.1471 0.00 826 27 0.1240 0.1168 REMARK 3 15 1.1471 - 1.1210 0.00 355 14 0.1426 0.1629 REMARK 3 16 1.1210 - 1.0972 0.00 134 4 0.1622 0.1080 REMARK 3 17 1.0972 - 1.0752 0.02 97 1 0.2048 0.0214 REMARK 3 18 1.0752 - 1.0550 0.01 44 2 0.2718 0.1162 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.52 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7TFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000261438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61983 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 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) : 0.52800 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: 5WBW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 2000, 5% PEG 3350, 5% PEG 4000, REMARK 280 5% PEGME 5000, 0.1 M KCL, 0.1 M MGCL2, 0.1 M PIPES PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 35.90350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.48550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.48550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.95175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.48550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.48550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.85525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.48550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.48550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.95175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.48550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.48550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.85525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.90350 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 385 LIES ON A SPECIAL POSITION. 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 THR A 2 REMARK 465 GLY A 145 REMARK 465 LYS A 146 REMARK 465 LYS A 147 REMARK 465 ILE A 148 REMARK 465 THR A 149 REMARK 465 SER A 150 REMARK 465 ASP A 151 REMARK 465 PHE A 152 REMARK 465 GLN A 153 REMARK 465 ASP A 154 REMARK 465 ASP A 155 REMARK 465 ASN A 156 REMARK 465 TYR A 157 REMARK 465 GLU A 158 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 THR A 137 OG1 CG2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 498 DISTANCE = 6.26 ANGSTROMS DBREF 7TFM A 1 158 UNP E9ALU6 E9ALU6_LEIMU 1 158 SEQRES 1 A 158 MET THR THR GLN GLN PRO GLU TRP THR GLN ALA ALA SER SEQRES 2 A 158 ASP LEU MET ALA ARG THR ALA ALA LEU ALA ARG LYS LYS SEQRES 3 A 158 ALA ASN GLY TYR LEU ASP PRO VAL HIS LEU ALA TYR VAL SEQRES 4 A 158 MET PHE GLU ASP GLU ASN SER LEU ALA SER ARG VAL VAL SEQRES 5 A 158 ARG LYS LEU GLY ALA ALA SER VAL LYS ASP GLY LEU GLU SEQRES 6 A 158 ALA ARG VAL ASP ALA ILE PRO THR GLN MET PRO ALA PRO SEQRES 7 A 158 THR GLN PRO ARG PRO ASN SER ASP MET MET ARG VAL MET SEQRES 8 A 158 ASN THR ALA GLU GLN GLU ARG VAL ALA LEU GLY ASP THR SEQRES 9 A 158 LEU MET ALA ALA ASP HIS PHE LEU LEU ALA LEU HIS GLU SEQRES 10 A 158 SER LYS GLU VAL GLY ARG ILE LEU ASP ALA ALA GLY ALA SEQRES 11 A 158 GLY LYS LYS ALA ILE ARG THR THR LEU LEU GLU MET ARG SEQRES 12 A 158 LYS GLY LYS LYS ILE THR SER ASP PHE GLN ASP ASP ASN SEQRES 13 A 158 TYR GLU HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *198(H2 O) HELIX 1 AA1 THR A 9 LYS A 26 1 18 HELIX 2 AA2 ASP A 32 ASP A 43 1 12 HELIX 3 AA3 SER A 46 GLY A 56 1 11 HELIX 4 AA4 VAL A 60 ALA A 70 1 11 HELIX 5 AA5 ASN A 84 GLY A 102 1 19 HELIX 6 AA6 ALA A 107 LEU A 115 1 9 HELIX 7 AA7 SER A 118 GLY A 129 1 12 HELIX 8 AA8 GLY A 131 ARG A 143 1 13 SHEET 1 AA1 2 TYR A 30 LEU A 31 0 SHEET 2 AA1 2 ARG A 82 PRO A 83 1 O ARG A 82 N LEU A 31 CISPEP 1 MET A 75 PRO A 76 0 2.27 CRYST1 60.971 60.971 71.807 90.00 90.00 90.00 P 41 21 2 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 0.016401 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013926 0.00000