HEADER SIGNALING PROTEIN 03-MAR-19 6JL3 TITLE CRYSTAL STRUCTURE OF THE UBL DOMAIN OF PLASMODIUM FALCIPARUM DSK2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN DOMAIN-CONTAINING PROTEIN DSK2,PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-77; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE INITIAL TWO AMINO ACID (MA) AND THE LAST THREE COMPND 7 AMINO ACID (AMA) ELECTRON DENSITY WERE MISSING. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_COMMON: ISOLATE 3D7; SOURCE 4 ORGANISM_TAXID: 36329; SOURCE 5 GENE: PF3D7_1113400; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI B83; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1151239; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B83; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: DE3; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS UBIQUITIN BINDING, SHUTTLE FACTOR, UBIQUITIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.GUPTA,S.KHAN REVDAT 4 22-NOV-23 6JL3 1 REMARK REVDAT 3 04-MAR-20 6JL3 1 JRNL REVDAT 2 26-FEB-20 6JL3 1 JRNL REVDAT 1 19-FEB-20 6JL3 0 JRNL AUTH I.GUPTA,S.KHAN JRNL TITL THE RECOGNITION OF PROTEASOMAL RECEPTORS BY PLASMODIUM JRNL TITL 2 FALCIPARUM DSK2. JRNL REF MOL.BIOCHEM.PARASITOL. V. 236 11266 2020 JRNL REFN ISSN 0166-6851 JRNL PMID 32057831 JRNL DOI 10.1016/J.MOLBIOPARA.2020.111266 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17995 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1800 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 0.0000 - 3.0639 1.00 1366 152 0.0000 0.1979 REMARK 3 2 3.0639 - 2.4321 1.00 1288 143 0.0000 0.1774 REMARK 3 3 2.4321 - 2.1247 1.00 1266 140 0.0000 0.1450 REMARK 3 4 2.1247 - 1.9304 1.00 1252 140 0.0000 0.1484 REMARK 3 5 1.9304 - 1.7921 1.00 1251 138 0.1313 0.1316 REMARK 3 6 1.7921 - 1.6864 1.00 1244 139 0.0000 0.1429 REMARK 3 7 1.6864 - 1.6020 1.00 1237 138 0.1292 0.1313 REMARK 3 8 1.6020 - 1.5322 1.00 1229 136 0.1245 0.1468 REMARK 3 9 1.5322 - 1.4732 1.00 1223 136 0.1266 0.1403 REMARK 3 10 1.4732 - 1.4224 1.00 1231 137 0.0000 0.1542 REMARK 3 11 1.4224 - 1.3779 1.00 1227 136 0.0000 0.2117 REMARK 3 12 1.3779 - 1.3385 1.00 1198 133 0.0000 0.2137 REMARK 3 13 1.3385 - 1.3033 0.95 1183 132 0.0000 0.2960 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.98 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 6JL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-18 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 : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18008 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.303 REMARK 200 RESOLUTION RANGE LOW (A) : 35.463 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.4700 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) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 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: PHENIX REMARK 200 STARTING MODEL: 2BWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 6.5 , 2M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 14.06100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.46350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.46350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 7.03050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.46350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.46350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.09150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.46350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.46350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 7.03050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.46350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.46350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.09150 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 14.06100 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 153 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 169 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 ALA A 2 REMARK 465 ALA A 77 REMARK 465 MET A 78 REMARK 465 ALA A 79 DBREF 6JL3 A 3 79 UNP Q8IIM8 Q8IIM8_PLAF7 1 77 SEQADV 6JL3 MET A 1 UNP Q8IIM8 INITIATING METHIONINE SEQADV 6JL3 ALA A 2 UNP Q8IIM8 EXPRESSION TAG SEQRES 1 A 79 MET ALA MET VAL ILE ASN VAL SER PHE LYS VAL THR GLY SEQRES 2 A 79 GLY LYS GLU PHE THR VAL ALA ILE GLU PRO ASP ILE THR SEQRES 3 A 79 VAL LEU ASP LEU LYS LYS ILE CYS ALA GLU HIS VAL ASP SEQRES 4 A 79 ILE PRO VAL GLU ALA GLN ARG ILE ILE PHE LYS GLY LYS SEQRES 5 A 79 ILE LEU LYS ASP LYS GLU SER LEU THR LEU TYR GLY VAL SEQRES 6 A 79 ALA ASP GLY ASN THR MET HIS LEU VAL ARG SER ALA MET SEQRES 7 A 79 ALA FORMUL 2 HOH *82(H2 O) HELIX 1 AA1 THR A 26 GLU A 36 1 11 HELIX 2 AA2 PRO A 41 GLU A 43 5 3 HELIX 3 AA3 SER A 59 GLY A 64 5 6 SHEET 1 AA1 5 LYS A 15 ILE A 21 0 SHEET 2 AA1 5 ILE A 5 VAL A 11 -1 N PHE A 9 O PHE A 17 SHEET 3 AA1 5 THR A 70 ARG A 75 1 O MET A 71 N SER A 8 SHEET 4 AA1 5 GLN A 45 PHE A 49 -1 N ILE A 48 O HIS A 72 SHEET 5 AA1 5 LYS A 52 ILE A 53 -1 O LYS A 52 N PHE A 49 CRYST1 70.927 70.927 28.122 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 0.014099 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014099 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035559 0.00000