HEADER HYDROLASE 17-SEP-12 4H4A TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF DROSOPHILA MELANOGASTER TITLE 2 ZUCCHINI COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL CARDIOLIPIN HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL FRAGMENT (UNP RESIDUES 89-253); COMPND 5 SYNONYM: MITOCHONDRIAL PHOSPHOLIPASE HOMOLOG, MITOPLD, PROTEIN COMPND 6 ZUCCHINI; COMPND 7 EC: 3.1.4.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: ZUC, CG12314; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM22 KEYWDS PHOSPHOLIPASE D FOLD, HKD MOTIF, NUCLEASE/PHOSPHOLIPID HYDROLASE, KEYWDS 2 NUCLEIC ACID/PHOSPHOLIPID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.VOIGT,E.C.SCHULZ,O.BARABAS REVDAT 3 15-NOV-17 4H4A 1 REMARK REVDAT 2 19-DEC-12 4H4A 1 JRNL REVDAT 1 07-NOV-12 4H4A 0 JRNL AUTH F.VOIGT,M.REUTER,A.KASARUHO,E.C.SCHULZ,R.S.PILLAI,O.BARABAS JRNL TITL CRYSTAL STRUCTURE OF THE PRIMARY PIRNA BIOGENESIS FACTOR JRNL TITL 2 ZUCCHINI REVEALS SIMILARITY TO THE BACTERIAL PLD JRNL TITL 3 ENDONUCLEASE NUC. JRNL REF RNA V. 18 2128 2012 JRNL REFN ISSN 1355-8382 JRNL PMID 23086923 JRNL DOI 10.1261/RNA.034967.112 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14002 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1383 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 33.9703 - 4.7362 1.00 1259 144 0.2401 0.2573 REMARK 3 2 4.7362 - 3.7609 0.99 1276 121 0.1856 0.1999 REMARK 3 3 3.7609 - 3.2859 1.00 1222 169 0.1854 0.2359 REMARK 3 4 3.2859 - 2.9857 1.00 1244 143 0.1996 0.2607 REMARK 3 5 2.9857 - 2.7718 1.00 1307 117 0.2217 0.2459 REMARK 3 6 2.7718 - 2.6084 1.00 1254 131 0.2531 0.2910 REMARK 3 7 2.6084 - 2.4778 1.00 1304 132 0.2392 0.3223 REMARK 3 8 2.4778 - 2.3700 1.00 1206 150 0.2415 0.3035 REMARK 3 9 2.3700 - 2.2788 1.00 1282 141 0.2488 0.3132 REMARK 3 10 2.2788 - 2.2002 1.00 1265 135 0.2836 0.3208 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 : 0.39 REMARK 3 B_SOL : 64.38 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.24690 REMARK 3 B22 (A**2) : -4.37810 REMARK 3 B33 (A**2) : 6.62510 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.17390 REMARK 3 B23 (A**2) : 0.00000 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 : 0.003 1159 REMARK 3 ANGLE : 0.667 1570 REMARK 3 CHIRALITY : 0.046 187 REMARK 3 PLANARITY : 0.002 198 REMARK 3 DIHEDRAL : 12.613 404 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 27.3336 38.5147 6.8911 REMARK 3 T TENSOR REMARK 3 T11: 0.1287 T22: 0.1598 REMARK 3 T33: 0.1545 T12: 0.0220 REMARK 3 T13: -0.0341 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 3.3029 L22: 2.6351 REMARK 3 L33: 2.8222 L12: 0.0868 REMARK 3 L13: 0.0798 L23: -0.4002 REMARK 3 S TENSOR REMARK 3 S11: -0.0719 S12: -0.3303 S13: 0.2330 REMARK 3 S21: 0.0819 S22: 0.1048 S23: 0.1419 REMARK 3 S31: -0.2075 S32: -0.1198 S33: -0.0526 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 4H4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075000. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942 REMARK 200 MONOCHROMATOR : MIRRORS + BARTELS MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14007 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 11.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54400 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW, SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.1M BIS-TRIS, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.64000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 THR A 165 REMARK 465 ASN A 166 REMARK 465 LEU A 190 REMARK 465 LYS A 191 REMARK 465 PHE A 192 REMARK 465 MSE A 193 REMARK 465 ALA A 209 REMARK 465 LEU A 210 REMARK 465 GLY A 211 REMARK 465 LEU A 212 REMARK 465 GLY A 213 REMARK 465 PHE A 242 REMARK 465 ALA A 243 REMARK 465 LYS A 244 REMARK 465 THR A 245 REMARK 465 GLU A 246 REMARK 465 GLY A 247 REMARK 465 SER A 248 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 MSE A 87 CG SE CE REMARK 470 ARG A 91 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 124 CG CD CE NZ REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 GLN A 154 CG CD OE1 NE2 REMARK 470 ILE A 163 CG1 CG2 CD1 REMARK 470 THR A 164 OG1 CG2 REMARK 470 LEU A 167 CG CD1 CD2 REMARK 470 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 ARG A 194 CG CD NE CZ NH1 NH2 REMARK 470 THR A 208 OG1 CG2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 ARG A 240 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 253 CG CD CE NZ 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 ILE A 163 90.17 60.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 4H4A A 89 253 UNP Q9VKD7 ZUC_DROME 89 253 SEQADV 4H4A GLY A 85 UNP Q9VKD7 CLONING ARTIFACT SEQADV 4H4A PRO A 86 UNP Q9VKD7 CLONING ARTIFACT SEQADV 4H4A MSE A 87 UNP Q9VKD7 CLONING ARTIFACT SEQADV 4H4A GLY A 88 UNP Q9VKD7 CLONING ARTIFACT SEQRES 1 A 169 GLY PRO MSE GLY SER LEU ARG ASN VAL ALA LYS ILE VAL SEQRES 2 A 169 GLU GLN ILE ASP ARG ALA VAL TYR SER ILE ASP LEU ALA SEQRES 3 A 169 ILE TYR THR PHE THR SER LEU PHE LEU ALA ASP SER ILE SEQRES 4 A 169 LYS ARG ALA LEU GLN ARG GLY VAL ILE ILE ARG ILE ILE SEQRES 5 A 169 SER ASP GLY GLU MSE VAL TYR SER LYS GLY SER GLN ILE SEQRES 6 A 169 SER MSE LEU ALA GLN LEU GLY VAL PRO VAL ARG VAL PRO SEQRES 7 A 169 ILE THR THR ASN LEU MSE HIS ASN LYS PHE CYS ILE ILE SEQRES 8 A 169 ASP GLY PHE GLU ARG VAL GLU GLU ILE ARG LEU LEU ARG SEQRES 9 A 169 LYS LEU LYS PHE MSE ARG PRO CYS TYR SER ILE VAL ILE SEQRES 10 A 169 SER GLY SER VAL ASN TRP THR ALA LEU GLY LEU GLY GLY SEQRES 11 A 169 ASN TRP GLU ASN CYS ILE ILE THR ALA ASP ASP LYS LEU SEQRES 12 A 169 THR ALA THR PHE GLN ALA GLU PHE GLN ARG MSE TRP ARG SEQRES 13 A 169 ALA PHE ALA LYS THR GLU GLY SER GLN ILE GLN LEU LYS MODRES 4H4A MSE A 87 MET SELENOMETHIONINE MODRES 4H4A MSE A 141 MET SELENOMETHIONINE MODRES 4H4A MSE A 151 MET SELENOMETHIONINE MODRES 4H4A MSE A 168 MET SELENOMETHIONINE MODRES 4H4A MSE A 238 MET SELENOMETHIONINE HET MSE A 87 5 HET MSE A 141 8 HET MSE A 151 8 HET MSE A 168 8 HET MSE A 238 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 HOH *40(H2 O) HELIX 1 1 GLY A 85 ALA A 103 1 19 HELIX 2 2 SER A 116 ARG A 129 1 14 HELIX 3 3 ASP A 138 VAL A 142 5 5 HELIX 4 4 GLN A 148 GLN A 154 1 7 HELIX 5 5 GLY A 177 LYS A 189 1 13 HELIX 6 6 ASP A 224 ALA A 241 1 18 SHEET 1 A 7 ILE A 220 THR A 222 0 SHEET 2 A 7 ILE A 199 GLY A 203 -1 N VAL A 200 O THR A 222 SHEET 3 A 7 LYS A 171 ILE A 175 -1 N ILE A 175 O ILE A 199 SHEET 4 A 7 SER A 106 ALA A 110 -1 N ASP A 108 O ILE A 174 SHEET 5 A 7 ILE A 132 ILE A 136 1 O ILE A 136 N LEU A 109 SHEET 6 A 7 VAL A 159 VAL A 161 1 O ARG A 160 N ILE A 135 SHEET 7 A 7 ILE A 250 GLN A 251 -1 O ILE A 250 N VAL A 161 LINK C PRO A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N GLY A 88 1555 1555 1.33 LINK C GLU A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N VAL A 142 1555 1555 1.33 LINK C SER A 150 N MSE A 151 1555 1555 1.33 LINK C MSE A 151 N LEU A 152 1555 1555 1.33 LINK C LEU A 167 N MSE A 168 1555 1555 1.33 LINK C MSE A 168 N HIS A 169 1555 1555 1.33 LINK C ARG A 237 N MSE A 238 1555 1555 1.33 LINK C MSE A 238 N TRP A 239 1555 1555 1.33 CISPEP 1 ILE A 163 THR A 164 0 0.40 CRYST1 35.640 51.280 40.970 90.00 107.63 90.00 P 1 21 1 2 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 0.028058 0.000000 0.008916 0.00000 SCALE2 0.000000 0.019501 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025611 0.00000