HEADER TRANSLATION 31-JUL-18 6H7A TITLE STRUCTURE OF LEISHMANIA PABP1 (DOMAIN J). COMPND MOL_ID: 1; COMPND 2 MOLECULE: PABP1 DOMAIN J; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: NICO21 KEYWDS COMPLEX TRANSLATION INITIATION LEISHMANIA, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR A.D.CAMERON,H.FIRCZUK,F.H.DOS SANTOS RODRIGUES,J.E.G.MCCARTHY REVDAT 3 17-JAN-24 6H7A 1 REMARK REVDAT 2 03-JUL-19 6H7A 1 JRNL REVDAT 1 12-DEC-18 6H7A 0 JRNL AUTH F.H.DOS SANTOS RODRIGUES,H.FIRCZUK,A.L.BREEZE,A.D.CAMERON, JRNL AUTH 2 M.WALKO,A.J.WILSON,N.I.T.ZANCHIN,J.E.G.MCCARTHY JRNL TITL THE LEISHMANIA PABP1-EIF4E4 INTERFACE: A NOVEL 5'-3' JRNL TITL 2 INTERACTION ARCHITECTURE FOR TRANS-SPLICED MRNAS. JRNL REF NUCLEIC ACIDS RES. V. 47 1493 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30476241 JRNL DOI 10.1093/NAR/GKY1187 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.350 REMARK 3 FREE R VALUE TEST SET COUNT : 632 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 27.1607 - 3.4694 1.00 2291 131 0.1778 0.2038 REMARK 3 2 3.4694 - 2.7546 1.00 2250 115 0.2209 0.2266 REMARK 3 3 2.7546 - 2.4066 1.00 2206 140 0.2203 0.2406 REMARK 3 4 2.4066 - 2.1867 1.00 2242 103 0.2192 0.2683 REMARK 3 5 2.1867 - 2.0300 1.00 2200 143 0.2581 0.2914 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.980 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 : 0.002 1294 REMARK 3 ANGLE : 0.423 1749 REMARK 3 CHIRALITY : 0.034 199 REMARK 3 PLANARITY : 0.004 228 REMARK 3 DIHEDRAL : 13.513 832 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 481 THROUGH 560) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2264 29.8167 19.8196 REMARK 3 T TENSOR REMARK 3 T11: 0.3402 T22: 0.3747 REMARK 3 T33: 0.3269 T12: 0.0051 REMARK 3 T13: 0.0305 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 7.9716 L22: 1.2101 REMARK 3 L33: 1.4651 L12: 0.7159 REMARK 3 L13: 1.3810 L23: -0.2363 REMARK 3 S TENSOR REMARK 3 S11: -0.0715 S12: -0.1197 S13: 0.0171 REMARK 3 S21: -0.1633 S22: -0.0001 S23: 0.0383 REMARK 3 S31: 0.1172 S32: -0.1901 S33: 0.0733 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 482 THROUGH 560) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3975 50.7230 25.5435 REMARK 3 T TENSOR REMARK 3 T11: 0.3320 T22: 0.3230 REMARK 3 T33: 0.3239 T12: 0.0097 REMARK 3 T13: -0.0191 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 4.2205 L22: 8.6974 REMARK 3 L33: 1.0236 L12: -4.2374 REMARK 3 L13: -1.3604 L23: 2.1002 REMARK 3 S TENSOR REMARK 3 S11: -0.0063 S12: -0.0094 S13: 0.1894 REMARK 3 S21: 0.1639 S22: -0.0253 S23: -0.1773 REMARK 3 S31: -0.1233 S32: -0.0216 S33: 0.0670 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 6H7A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200011203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9760 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11824 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.90 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 19.80 REMARK 200 R MERGE FOR SHELL (I) : 1.82100 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: 3PTH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM REMARK 280 CACODYLATE AT PH 6.5, 30% PEG8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.72000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.36000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.04000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.68000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.40000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 469 REMARK 465 HIS A 470 REMARK 465 HIS A 471 REMARK 465 HIS A 472 REMARK 465 HIS A 473 REMARK 465 HIS A 474 REMARK 465 HIS A 475 REMARK 465 HIS A 476 REMARK 465 HIS A 477 REMARK 465 HIS A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 MET B 469 REMARK 465 HIS B 470 REMARK 465 HIS B 471 REMARK 465 HIS B 472 REMARK 465 HIS B 473 REMARK 465 HIS B 474 REMARK 465 HIS B 475 REMARK 465 HIS B 476 REMARK 465 HIS B 477 REMARK 465 HIS B 478 REMARK 465 HIS B 479 REMARK 465 HIS B 480 REMARK 465 HIS B 481 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 O HOH B 630 O HOH B 635 1.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 6H7A A 482 560 UNP E9AFX7 E9AFX7_LEIMA 482 560 DBREF 6H7A B 482 560 UNP E9AFX7 E9AFX7_LEIMA 482 560 SEQADV 6H7A MET A 469 UNP E9AFX7 INITIATING METHIONINE SEQADV 6H7A HIS A 470 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 471 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 472 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 473 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 474 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 475 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 476 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 477 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 478 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 479 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 480 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS A 481 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A MET B 469 UNP E9AFX7 INITIATING METHIONINE SEQADV 6H7A HIS B 470 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 471 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 472 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 473 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 474 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 475 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 476 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 477 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 478 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 479 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 480 UNP E9AFX7 EXPRESSION TAG SEQADV 6H7A HIS B 481 UNP E9AFX7 EXPRESSION TAG SEQRES 1 A 92 MET HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 2 A 92 LEU PRO PRO ILE THR PRO GLN GLU LEU GLU SER MET SER SEQRES 3 A 92 PRO GLN GLU GLN ARG ALA ALA LEU GLY ASP ARG LEU PHE SEQRES 4 A 92 LEU LYS VAL TYR GLU ILE ALA PRO GLU LEU ALA PRO LYS SEQRES 5 A 92 ILE THR GLY MET PHE LEU GLU MET LYS PRO LYS GLU ALA SEQRES 6 A 92 TYR GLU LEU LEU ASN ASP GLN LYS ARG LEU GLU GLU ARG SEQRES 7 A 92 VAL THR GLU ALA LEU CYS VAL LEU LYS ALA HIS GLN THR SEQRES 8 A 92 ALA SEQRES 1 B 92 MET HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 2 B 92 LEU PRO PRO ILE THR PRO GLN GLU LEU GLU SER MET SER SEQRES 3 B 92 PRO GLN GLU GLN ARG ALA ALA LEU GLY ASP ARG LEU PHE SEQRES 4 B 92 LEU LYS VAL TYR GLU ILE ALA PRO GLU LEU ALA PRO LYS SEQRES 5 B 92 ILE THR GLY MET PHE LEU GLU MET LYS PRO LYS GLU ALA SEQRES 6 B 92 TYR GLU LEU LEU ASN ASP GLN LYS ARG LEU GLU GLU ARG SEQRES 7 B 92 VAL THR GLU ALA LEU CYS VAL LEU LYS ALA HIS GLN THR SEQRES 8 B 92 ALA FORMUL 3 HOH *72(H2 O) HELIX 1 AA1 THR A 486 MET A 493 1 8 HELIX 2 AA2 SER A 494 GLU A 512 1 19 HELIX 3 AA3 LEU A 517 LEU A 526 1 10 HELIX 4 AA4 LYS A 529 ASP A 539 1 11 HELIX 5 AA5 ASP A 539 HIS A 557 1 19 HELIX 6 AA6 THR B 486 MET B 493 1 8 HELIX 7 AA7 SER B 494 GLU B 512 1 19 HELIX 8 AA8 LEU B 517 LEU B 526 1 10 HELIX 9 AA9 LYS B 529 LEU B 537 1 9 HELIX 10 AB1 ASP B 539 HIS B 557 1 19 SSBOND 1 CYS A 552 CYS B 552 1555 1555 2.03 CRYST1 82.970 82.970 46.080 90.00 90.00 120.00 P 65 12 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 0.012053 0.006959 0.000000 0.00000 SCALE2 0.000000 0.013917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021701 0.00000