HEADER RNA BINDING PROTEIN/RNA 01-AUG-10 3O7V TITLE CRYSTAL STRUCTURE OF HUMAN HIWI1 (V361M) PAZ DOMAIN (RESIDUES 277-399) TITLE 2 IN COMPLEX WITH 14-MER RNA (12-BP + 2-NT OVERHANG) CONTAINING 2'-OCH3 TITLE 3 AT ITS 3'-END COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI-LIKE PROTEIN 1; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: PAZ DOMAIN (UNP RESIDUES 276-399); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*(OMU))- COMPND 9 3'); COMPND 10 CHAIN: A; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HIWI, PIWI-LIKE PROTEIN 1, PIWIL1; 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: PET-28B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS PIWI, RNA SILENCING, PI-RNA, HIWI1, HILI, PAZ DOMAIN, RNA BINDING KEYWDS 2 PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.TIAN,D.K.SIMANSHU,J.-B.MA,D.J.PATEL REVDAT 3 08-NOV-17 3O7V 1 REMARK REVDAT 2 02-FEB-11 3O7V 1 JRNL REVDAT 1 12-JAN-11 3O7V 0 JRNL AUTH Y.TIAN,D.K.SIMANSHU,J.B.MA,D.J.PATEL JRNL TITL INAUGURAL ARTICLE: STRUCTURAL BASIS FOR PIRNA JRNL TITL 2 2'-O-METHYLATED 3'-END RECOGNITION BY PIWI PAZ JRNL TITL 3 (PIWI/ARGONAUTE/ZWILLE) DOMAINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 903 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21193640 JRNL DOI 10.1073/PNAS.1017762108 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9194 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 450 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) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 595 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 874 REMARK 3 NUCLEIC ACID ATOMS : 293 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.20000 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): 0.282 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.624 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1220 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1714 ; 1.383 ; 2.266 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 105 ; 6.256 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 44 ;33.082 ;25.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 158 ;16.631 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;15.761 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 201 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 815 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 534 ; 0.606 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 866 ; 1.170 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 686 ; 1.672 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 848 ; 2.420 ; 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 : 2 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 : X -10 X 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 11.3385 24.4058 62.9260 REMARK 3 T TENSOR REMARK 3 T11: 0.0522 T22: 0.1792 REMARK 3 T33: 0.0561 T12: 0.0126 REMARK 3 T13: -0.0124 T23: 0.0534 REMARK 3 L TENSOR REMARK 3 L11: 2.0923 L22: 5.8422 REMARK 3 L33: 3.0539 L12: 0.4516 REMARK 3 L13: 0.1870 L23: 2.2341 REMARK 3 S TENSOR REMARK 3 S11: 0.0454 S12: -0.1910 S13: -0.0287 REMARK 3 S21: 0.1047 S22: 0.0633 S23: 0.2038 REMARK 3 S31: 0.0311 S32: -0.4544 S33: -0.1087 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 32.2999 36.7495 58.5363 REMARK 3 T TENSOR REMARK 3 T11: 0.2067 T22: 0.2390 REMARK 3 T33: 0.4804 T12: -0.0036 REMARK 3 T13: 0.0354 T23: -0.1480 REMARK 3 L TENSOR REMARK 3 L11: 6.0570 L22: 0.1117 REMARK 3 L33: 0.5773 L12: 0.6180 REMARK 3 L13: -1.8190 L23: -0.2099 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: -0.3346 S13: 0.2747 REMARK 3 S21: 0.0202 S22: -0.0171 S23: -0.1137 REMARK 3 S31: 0.0012 S32: 0.1484 S33: -0.0255 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 3O7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060775. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CRYO-COOLED SI(111) DOUBLE REMARK 200 CRYSTAL. REMARK 200 OPTICS : CRYOGENICALLY-COOLED DOUBLE REMARK 200 CRYSTAL SI(111) MONOCHROMATOR. REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9244 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.4000 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) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-5% PEG3350, 50 MM NACL, 50 MM NA REMARK 280 -ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 73.59850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.79925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 110.39775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.59850 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 110.39775 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 36.79925 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, 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 110.39775 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 SER X 276 REMARK 465 ARG X 368 REMARK 465 ARG X 369 REMARK 465 ARG X 370 REMARK 465 GLY X 371 REMARK 465 PRO X 372 REMARK 465 GLY X 373 REMARK 465 GLY X 374 REMARK 465 THR X 375 REMARK 465 LEU X 376 REMARK 465 PRO X 377 REMARK 465 ASP X 394 REMARK 465 LYS X 395 REMARK 465 MET X 396 REMARK 465 ARG X 397 REMARK 465 ASN X 398 REMARK 465 ASP X 399 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 GLN X 298 OE1 NE2 REMARK 470 LYS X 301 CG CD CE NZ REMARK 470 GLU X 302 CG CD OE1 OE2 REMARK 470 GLU X 339 CG CD OE1 OE2 REMARK 470 LEU X 392 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G A 3 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 G A 3 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 G A 3 C4' - C3' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 A A 7 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES 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 PRO X 366 -172.65 -58.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3O3I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HIWI1 PAZ DOMAIN (RESIDUES 277-399) IN REMARK 900 COMPLEX WITH 14-MER RNA (12-BP + 2-NT OVERHANG) CONTAINING 2'-OH AT REMARK 900 ITS 3'-END REMARK 900 RELATED ID: 3O6E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HIWI1 PAZ DOMAIN (RESIDUES 277-399) IN REMARK 900 COMPLEX WITH 14-MER RNA (12-BP + 2-NT OVERHANG) CONTAINING 2'-OCH3 REMARK 900 AT ITS 3'-END REMARK 900 RELATED ID: 3O7X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HILI PAZ DOMAIN (RESIDUES 277-399) DBREF 3O7V X 276 399 UNP Q96J94 PIWL1_HUMAN 276 399 DBREF 3O7V A 1 14 PDB 3O7V 3O7V 1 14 SEQADV 3O7V MSE X 361 UNP Q96J94 VAL 361 ENGINEERED MUTATION SEQRES 1 X 124 SER GLU THR VAL LEU ASP PHE MSE PHE ASN PHE TYR HIS SEQRES 2 X 124 GLN THR GLU GLU HIS LYS PHE GLN GLU GLN VAL SER LYS SEQRES 3 X 124 GLU LEU ILE GLY LEU VAL VAL LEU THR LYS TYR ASN ASN SEQRES 4 X 124 LYS THR TYR ARG VAL ASP ASP ILE ASP TRP ASP GLN ASN SEQRES 5 X 124 PRO LYS SER THR PHE LYS LYS ALA ASP GLY SER GLU VAL SEQRES 6 X 124 SER PHE LEU GLU TYR TYR ARG LYS GLN TYR ASN GLN GLU SEQRES 7 X 124 ILE THR ASP LEU LYS GLN PRO MSE LEU VAL SER GLN PRO SEQRES 8 X 124 LYS ARG ARG ARG GLY PRO GLY GLY THR LEU PRO GLY PRO SEQRES 9 X 124 ALA MSE LEU ILE PRO GLU LEU CYS TYR LEU THR GLY LEU SEQRES 10 X 124 THR ASP LYS MET ARG ASN ASP SEQRES 1 A 14 G C G A A U A U U C G C U SEQRES 2 A 14 OMU MODRES 3O7V MSE X 283 MET SELENOMETHIONINE MODRES 3O7V MSE X 361 MET SELENOMETHIONINE MODRES 3O7V MSE X 381 MET SELENOMETHIONINE MODRES 3O7V OMU A 14 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE HET MSE X 283 8 HET MSE X 361 8 HET MSE X 381 8 HET OMU A 14 21 HETNAM MSE SELENOMETHIONINE HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 OMU C10 H15 N2 O9 P FORMUL 3 HOH *52(H2 O) HELIX 1 1 THR X 278 PHE X 286 1 9 HELIX 2 2 GLU X 291 ILE X 304 1 14 HELIX 3 3 PHE X 342 ASN X 351 1 10 HELIX 4 4 ILE X 383 GLU X 385 5 3 SHEET 1 A 3 THR X 316 ARG X 318 0 SHEET 2 A 3 VAL X 307 THR X 310 -1 N VAL X 308 O TYR X 317 SHEET 3 A 3 CYS X 387 TYR X 388 -1 O TYR X 388 N LEU X 309 SHEET 1 B 3 ASP X 321 ASP X 323 0 SHEET 2 B 3 MSE X 361 SER X 364 -1 O VAL X 363 N ASP X 321 SHEET 3 B 3 ALA X 380 LEU X 382 -1 O LEU X 382 N LEU X 362 SHEET 1 C 2 THR X 331 LYS X 333 0 SHEET 2 C 2 GLU X 339 SER X 341 -1 O VAL X 340 N PHE X 332 LINK C PHE X 282 N MSE X 283 1555 1555 1.34 LINK C MSE X 283 N PHE X 284 1555 1555 1.32 LINK C PRO X 360 N MSE X 361 1555 1555 1.33 LINK C MSE X 361 N LEU X 362 1555 1555 1.33 LINK C ALA X 380 N MSE X 381 1555 1555 1.33 LINK C MSE X 381 N LEU X 382 1555 1555 1.32 LINK O3' U A 13 P OMU A 14 1555 1555 1.60 CRYST1 44.460 44.460 147.197 90.00 90.00 90.00 P 41 2 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 0.022492 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006794 0.00000