HEADER RNA BINDING PROTEIN 03-DEC-15 5F3P TITLE CRYSTAL STRUCTURE OF A NONCANONICAL DICER PROTEIN FROM ENTAMOEBA TITLE 2 HISTOLYTICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 2-195; COMPND 5 SYNONYM: EHRNASEIII; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTAMOEBA HISTOLYTICA; SOURCE 3 ORGANISM_TAXID: 5759; SOURCE 4 GENE: EHI_068740; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASEIII, NON CANONICAL DICER, RNA PROCESING, ENTAMOEBA HISTOLYTICA, KEYWDS 2 RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.YU,J.H.GAN,J.B.MA REVDAT 2 20-MAR-24 5F3P 1 REMARK REVDAT 1 08-FEB-17 5F3P 0 JRNL AUTH X.YU,J.H.GAN,J.B.MA JRNL TITL STRUCTURAL AND FUNCTIONAL STUDY OF A NONCANONICAL DICER JRNL TITL 2 PROTEIN IN ENTAMOEBA HISTOLYTICA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 31554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1592 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 28.7336 - 4.2294 0.96 2921 171 0.1917 0.2258 REMARK 3 2 4.2294 - 3.3587 0.84 2476 130 0.1844 0.1889 REMARK 3 3 3.3587 - 2.9346 1.00 2907 158 0.1980 0.2393 REMARK 3 4 2.9346 - 2.6665 1.00 2894 148 0.1952 0.2386 REMARK 3 5 2.6665 - 2.4755 1.00 2875 143 0.1831 0.2595 REMARK 3 6 2.4755 - 2.3296 1.00 2876 147 0.1758 0.1871 REMARK 3 7 2.3296 - 2.2130 0.65 1853 95 0.2299 0.3392 REMARK 3 8 2.2130 - 2.1167 1.00 2862 149 0.1652 0.1929 REMARK 3 9 2.1167 - 2.0352 1.00 2832 152 0.1819 0.2188 REMARK 3 10 2.0352 - 1.9650 1.00 2846 153 0.2412 0.2483 REMARK 3 11 1.9650 - 1.9036 0.93 2620 146 0.5358 0.5449 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.730 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 : 0.008 3228 REMARK 3 ANGLE : 0.804 4357 REMARK 3 CHIRALITY : 0.042 473 REMARK 3 PLANARITY : 0.005 546 REMARK 3 DIHEDRAL : 15.481 1916 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 5F3P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000215921. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4-7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31630 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 94.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M (NH4)2SO4, 0.01 M MGCL2, 0.05 M REMARK 280 TRIS-HCL PH 7.5, VAPOR DIFFUSION, SITTING DROP, 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 23.04600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.17900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.97800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.17900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.04600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.97800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 1 REMARK 465 GLN A 43 REMARK 465 ASP B 105 REMARK 465 THR B 106 REMARK 465 LYS B 107 REMARK 465 THR B 108 REMARK 465 PHE B 109 REMARK 465 ASP B 194 REMARK 465 PRO B 195 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 GLU B 74 CB CG CD OE1 OE2 REMARK 470 GLN B 75 CB CG CD OE1 NE2 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 OE2 GLU A 79 O HOH A 301 1.87 REMARK 500 NZ LYS A 166 O HOH A 302 2.05 REMARK 500 NZ LYS A 72 O HOH A 303 2.05 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 GLU A 132 10.14 -140.47 REMARK 500 LEU A 164 -40.99 64.50 REMARK 500 ALA B 134 48.54 -156.21 REMARK 500 LEU B 164 -37.12 65.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F3Q RELATED DB: PDB REMARK 900 RELATED ID: 5F3O RELATED DB: PDB DBREF 5F3P A 2 195 UNP C4LU64 C4LU64_ENTHI 2 195 DBREF 5F3P B 2 195 UNP C4LU64 C4LU64_ENTHI 2 195 SEQADV 5F3P MET A 1 UNP C4LU64 INITIATING METHIONINE SEQADV 5F3P MET B 1 UNP C4LU64 INITIATING METHIONINE SEQRES 1 A 195 MET SER SER THR THR LEU HIS ASN ALA MET GLN TYR THR SEQRES 2 A 195 ALA PHE ASP VAL LEU SER SER ILE LEU ASN LEU MET LYS SEQRES 3 A 195 ALA ASP PRO LEU TYR ASP LEU LEU GLN LEU ASN GLN ALA SEQRES 4 A 195 TYR SER SER GLN ASP GLN GLU TYR GLU LYS ASN GLU PHE SEQRES 5 A 195 TYR GLY ASP SER TYR LEU GLU GLU ARG ALA SER SER LEU SEQRES 6 A 195 VAL LEU LYS PHE LEU ARG LYS TYR GLU GLN ILE PRO PHE SEQRES 7 A 195 GLU MET TYR SER GLY LEU ARG ILE HIS THR VAL LYS ASN SEQRES 8 A 195 GLN THR LEU GLY GLU ILE PHE ASP LEU LEU HIS LEU GLY SEQRES 9 A 195 ASP THR LYS THR PHE GLU LYS LYS LYS LYS GLY ASP LEU SEQRES 10 A 195 VAL GLU SER LEU ILE GLY GLY CYS VAL LEU LEU SER GLN SEQRES 11 A 195 ARG GLU ASN ALA THR LEU PHE LEU LEU PHE ALA HIS ALA SEQRES 12 A 195 LEU ILE ASP TYR ILE PHE TYR HIS SER SER TYR ILE TYR SEQRES 13 A 195 PHE ASN ALA ASN PRO PRO LYS LEU VAL LYS GLU GLU ILE SEQRES 14 A 195 ILE THR ASP ILE GLN ASN TRP PHE LYS ASP LYS LEU PHE SEQRES 15 A 195 TYR TYR ARG SER SER LEU GLU LYS TYR GLN THR ASP PRO SEQRES 1 B 195 MET SER SER THR THR LEU HIS ASN ALA MET GLN TYR THR SEQRES 2 B 195 ALA PHE ASP VAL LEU SER SER ILE LEU ASN LEU MET LYS SEQRES 3 B 195 ALA ASP PRO LEU TYR ASP LEU LEU GLN LEU ASN GLN ALA SEQRES 4 B 195 TYR SER SER GLN ASP GLN GLU TYR GLU LYS ASN GLU PHE SEQRES 5 B 195 TYR GLY ASP SER TYR LEU GLU GLU ARG ALA SER SER LEU SEQRES 6 B 195 VAL LEU LYS PHE LEU ARG LYS TYR GLU GLN ILE PRO PHE SEQRES 7 B 195 GLU MET TYR SER GLY LEU ARG ILE HIS THR VAL LYS ASN SEQRES 8 B 195 GLN THR LEU GLY GLU ILE PHE ASP LEU LEU HIS LEU GLY SEQRES 9 B 195 ASP THR LYS THR PHE GLU LYS LYS LYS LYS GLY ASP LEU SEQRES 10 B 195 VAL GLU SER LEU ILE GLY GLY CYS VAL LEU LEU SER GLN SEQRES 11 B 195 ARG GLU ASN ALA THR LEU PHE LEU LEU PHE ALA HIS ALA SEQRES 12 B 195 LEU ILE ASP TYR ILE PHE TYR HIS SER SER TYR ILE TYR SEQRES 13 B 195 PHE ASN ALA ASN PRO PRO LYS LEU VAL LYS GLU GLU ILE SEQRES 14 B 195 ILE THR ASP ILE GLN ASN TRP PHE LYS ASP LYS LEU PHE SEQRES 15 B 195 TYR TYR ARG SER SER LEU GLU LYS TYR GLN THR ASP PRO HET SO4 A 201 5 HET SO4 B 201 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *76(H2 O) HELIX 1 AA1 SER A 2 ALA A 27 1 26 HELIX 2 AA2 ASP A 28 SER A 41 5 14 HELIX 3 AA3 GLN A 45 ARG A 71 1 27 HELIX 4 AA4 PRO A 77 LYS A 90 1 14 HELIX 5 AA5 LYS A 90 LEU A 101 1 12 HELIX 6 AA6 GLU A 110 ASN A 133 1 24 HELIX 7 AA7 ALA A 134 ASN A 160 1 27 HELIX 8 AA8 VAL A 165 ASP A 194 1 30 HELIX 9 AA9 SER B 2 LYS B 26 1 25 HELIX 10 AB1 ASP B 32 LEU B 36 5 5 HELIX 11 AB2 SER B 42 ARG B 71 1 30 HELIX 12 AB3 PHE B 78 LYS B 90 1 13 HELIX 13 AB4 LYS B 90 LEU B 101 1 12 HELIX 14 AB5 LYS B 111 GLU B 132 1 22 HELIX 15 AB6 ALA B 134 ASN B 160 1 27 HELIX 16 AB7 VAL B 165 THR B 193 1 29 SITE 1 AC1 3 LYS A 68 TRP A 176 LYS A 180 SITE 1 AC2 4 LYS B 68 TRP B 176 LYS B 180 HOH B 302 CRYST1 46.092 89.956 100.358 90.00 90.00 90.00 P 21 21 21 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 0.021696 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009964 0.00000