HEADER HYDROLASE 06-AUG-12 4GGK TITLE CRYSTAL STRUCTURE OF ZUCCHINI FROM MOUSE (MZUC / PLD6 / MITOPLD) BOUND TITLE 2 TO TUNGSTATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL CARDIOLIPIN HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYTOPLASMIC DOMAIN, UNP RESIDUES 31-221; COMPND 5 SYNONYM: CHOLINE PHOSPHATASE 6, MITOCHONDRIAL PHOSPHOLIPASE, MITOPLD, COMPND 6 PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D6, PHOSPHOLIPASE D6, COMPND 7 PLD 6; COMPND 8 EC: 3.1.4.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PLD6; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFL KEYWDS PIRNA PATHWAY, PROTEIN-RNA INTERACTIONS, PIRNA BIOGENESIS, RNA KEYWDS 2 INTERFERENCE, RNAI, HKD MOTIF CCCH ZINC FINGER, NUCLEASE, NUCLEIC KEYWDS 3 ACID BINDING, OUTER MITOCHONDRIAL MEMBRANE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.J.IPSARO,A.D.HAASE,G.J.HANNON,L.JOSHUA-TOR REVDAT 3 13-SEP-23 4GGK 1 REMARK SEQADV LINK REVDAT 2 12-DEC-12 4GGK 1 JRNL REVDAT 1 10-OCT-12 4GGK 0 JRNL AUTH J.J.IPSARO,A.D.HAASE,S.R.KNOTT,L.JOSHUA-TOR,G.J.HANNON JRNL TITL THE STRUCTURAL BIOCHEMISTRY OF ZUCCHINI IMPLICATES IT AS A JRNL TITL 2 NUCLEASE IN PIRNA BIOGENESIS. JRNL REF NATURE V. 491 279 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 23064227 JRNL DOI 10.1038/NATURE11502 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9676 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 514 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 565 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1316 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.254 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.951 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1352 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 941 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1818 ; 1.382 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2268 ; 0.884 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 161 ; 6.462 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 65 ;42.316 ;22.923 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 238 ;14.372 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.486 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 207 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1465 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 284 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 535 ; 0.551 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 219 ; 0.132 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 857 ; 0.998 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 317 ; 1.695 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 292 ; 2.779 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 36 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): -10.3089 -15.4007 -12.2358 REMARK 3 T TENSOR REMARK 3 T11: 0.0484 T22: 0.0696 REMARK 3 T33: 0.0300 T12: -0.0124 REMARK 3 T13: -0.0006 T23: -0.0277 REMARK 3 L TENSOR REMARK 3 L11: 5.2756 L22: 2.6755 REMARK 3 L33: 3.4310 L12: -1.1767 REMARK 3 L13: -0.1849 L23: -0.4657 REMARK 3 S TENSOR REMARK 3 S11: 0.0673 S12: 0.4078 S13: -0.2012 REMARK 3 S21: -0.2536 S22: -0.0997 S23: -0.0417 REMARK 3 S31: -0.1366 S32: 0.0669 S33: 0.0324 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4GGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-12 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 : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2716, 1.2983 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR WITH REMARK 200 HORIZONTAL FOCUSING SAGITTAL REMARK 200 BEND SECOND MONO CRYSTAL WITH 4: REMARK 200 1 MAGNIFICATION RATIO AND REMARK 200 VERTICALLY FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10188 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 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: PDB ENTRY 1BYR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM BIS-TRIS, PH 6.5, 18% PEG-3350, REMARK 280 2% TASCIMATE, PH 6.0, 1:100 M/M RATIO PROTEIN:CHYMOTRYPSIN, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 106.65500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.42950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.42950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 159.98250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.42950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.42950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.32750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.42950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.42950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 159.98250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.42950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.42950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.32750 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 106.65500 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: 3180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 W WO4 A 302 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 30 REMARK 465 LEU A 31 REMARK 465 ALA A 32 REMARK 465 GLY A 33 REMARK 465 ARG A 34 REMARK 465 ARG A 35 REMARK 465 LEU A 59 REMARK 465 PRO A 60 REMARK 465 PRO A 61 REMARK 465 GLY A 62 REMARK 465 PRO A 63 REMARK 465 SER A 64 REMARK 465 GLY A 65 REMARK 465 ALA A 127 REMARK 465 LEU A 128 REMARK 465 ASN A 129 REMARK 465 LYS A 210 REMARK 465 TYR A 211 REMARK 465 SER A 212 REMARK 465 PHE A 213 REMARK 465 PHE A 214 REMARK 465 PRO A 215 REMARK 465 GLN A 216 REMARK 465 LYS A 217 REMARK 465 HIS A 218 REMARK 465 ARG A 219 REMARK 465 GLY A 220 REMARK 465 HIS A 221 REMARK 465 LEU A 222 REMARK 465 VAL A 223 REMARK 465 PRO A 224 REMARK 465 ARG A 225 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 HIS A 72 53.85 -102.09 REMARK 500 SER A 89 -41.45 -145.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 66 SG 119.3 REMARK 620 3 CYS A 68 SG 105.2 111.5 REMARK 620 4 HIS A 72 NE2 106.6 102.3 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 WO4 A 302 W REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 153 NE2 REMARK 620 2 WO4 A 302 O1 67.7 REMARK 620 3 WO4 A 302 O2 161.9 107.2 REMARK 620 4 WO4 A 302 O3 59.7 111.2 109.6 REMARK 620 5 WO4 A 302 O4 87.7 109.1 110.2 109.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WO4 A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BYR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUC (DSDNASE) REMARK 900 RELATED ID: 1BYS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUC (DSDNASE) IN COMPLEX WITH TUNGSTATE REMARK 900 RELATED ID: 4GGJ RELATED DB: PDB DBREF 4GGK A 31 221 UNP Q5SWZ9 PLD6_MOUSE 31 221 SEQADV 4GGK MET A 30 UNP Q5SWZ9 EXPRESSION TAG SEQADV 4GGK LEU A 222 UNP Q5SWZ9 EXPRESSION TAG SEQADV 4GGK VAL A 223 UNP Q5SWZ9 EXPRESSION TAG SEQADV 4GGK PRO A 224 UNP Q5SWZ9 EXPRESSION TAG SEQADV 4GGK ARG A 225 UNP Q5SWZ9 EXPRESSION TAG SEQRES 1 A 196 MET LEU ALA GLY ARG ARG PRO ARG ARG GLU VAL LEU PHE SEQRES 2 A 196 PHE PRO SER GLN VAL THR CYS THR GLU ALA LEU LEU GLN SEQRES 3 A 196 ALA PRO GLY LEU PRO PRO GLY PRO SER GLY CYS PRO CYS SEQRES 4 A 196 SER LEU PRO HIS SER GLU SER SER LEU SER ARG LEU LEU SEQRES 5 A 196 ARG ALA LEU LEU ALA ALA ARG SER SER LEU GLU LEU CYS SEQRES 6 A 196 LEU PHE ALA PHE SER SER PRO GLN LEU GLY ARG ALA VAL SEQRES 7 A 196 GLN LEU LEU HIS GLN ARG GLY VAL ARG VAL ARG VAL ILE SEQRES 8 A 196 THR ASP CYS ASP TYR MET ALA LEU ASN GLY SER GLN ILE SEQRES 9 A 196 GLY LEU LEU ARG LYS ALA GLY ILE GLN VAL ARG HIS ASP SEQRES 10 A 196 GLN ASP LEU GLY TYR MET HIS HIS LYS PHE ALA ILE VAL SEQRES 11 A 196 ASP LYS LYS VAL LEU ILE THR GLY SER LEU ASN TRP THR SEQRES 12 A 196 THR GLN ALA ILE GLN ASN ASN ARG GLU ASN VAL LEU ILE SEQRES 13 A 196 MET GLU ASP THR GLU TYR VAL ARG LEU PHE LEU GLU GLU SEQRES 14 A 196 PHE GLU ARG ILE TRP GLU GLU PHE ASP PRO THR LYS TYR SEQRES 15 A 196 SER PHE PHE PRO GLN LYS HIS ARG GLY HIS LEU VAL PRO SEQRES 16 A 196 ARG HET ZN A 301 1 HET WO4 A 302 5 HETNAM ZN ZINC ION HETNAM WO4 TUNGSTATE(VI)ION FORMUL 2 ZN ZN 2+ FORMUL 3 WO4 O4 W 2- FORMUL 4 HOH *35(H2 O) HELIX 1 1 SER A 75 ALA A 86 1 12 HELIX 2 2 SER A 100 ARG A 113 1 14 HELIX 3 3 SER A 131 ALA A 139 1 9 HELIX 4 4 THR A 172 ASN A 179 1 8 HELIX 5 5 ASP A 188 PHE A 206 1 19 SHEET 1 A 7 ARG A 38 PHE A 43 0 SHEET 2 A 7 GLU A 181 MET A 186 -1 O VAL A 183 N LEU A 41 SHEET 3 A 7 VAL A 163 GLY A 167 -1 N LEU A 164 O MET A 186 SHEET 4 A 7 LYS A 155 VAL A 159 -1 N ALA A 157 O ILE A 165 SHEET 5 A 7 SER A 90 LEU A 95 -1 N CYS A 94 O PHE A 156 SHEET 6 A 7 ARG A 116 THR A 121 1 O ILE A 120 N LEU A 93 SHEET 7 A 7 GLN A 142 HIS A 145 1 O ARG A 144 N VAL A 119 LINK SG CYS A 49 ZN ZN A 301 1555 1555 2.29 LINK SG CYS A 66 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 68 ZN ZN A 301 1555 1555 2.35 LINK NE2 HIS A 72 ZN ZN A 301 1555 1555 2.09 LINK NE2 HIS A 153 W WO4 A 302 1555 1555 3.03 CISPEP 1 PHE A 43 PRO A 44 0 11.29 SITE 1 AC1 4 CYS A 49 CYS A 66 CYS A 68 HIS A 72 SITE 1 AC2 4 PHE A 96 HIS A 153 LYS A 155 ASN A 170 CRYST1 38.859 38.859 213.310 90.00 90.00 90.00 P 43 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 0.025734 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004688 0.00000