HEADER HYDROLASE/RNA 02-FEB-14 4OOG TITLE CRYSTAL STRUCTURE OF YEAST RNASE III (RNT1P) COMPLEXED WITH THE TITLE 2 PRODUCT OF DSRNA PROCESSING COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 42-151); COMPND 5 SYNONYM: RIBONUCLEASE III, RNASE III; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RIBONUCLEASE 3; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: ENDONUCLEASE DOMAIN AND DOUBLE-STRANDED RNA BINDING DOMAIN COMPND 11 (UNP RESIDUES 197-457); COMPND 12 SYNONYM: RIBONUCLEASE III, RNASE III; COMPND 13 EC: 3.1.26.3; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 34-MER RNA; COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: RNT1, YM9408.01C, YM9959.21, YMR239C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1007065; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE31; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 14 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 15 ORGANISM_TAXID: 559292; SOURCE 16 STRAIN: ATCC 204508 / S288C; SOURCE 17 GENE: RNT1, YM9408.01C, YM9959.21, YMR239C; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 1007065; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PQE31; SOURCE 23 MOL_ID: 3; SOURCE 24 SYNTHETIC: YES; SOURCE 25 OTHER_DETAILS: DERIVED FROM U5 SNRNA 3' END CLEAVAGE PRODUCT KEYWDS RNASE:RNA COMPLEX, RIBONUCLEASE III DOMAIN, DOUBLE-STRANDED RNA- KEYWDS 2 BINDING DOMAIN, ENDORIBONUCLEASE, DSRNA-SPECIFIC RNASE, DOUBLE- KEYWDS 3 STRANDED RNA, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-H.LIANG,X.JI REVDAT 4 20-SEP-23 4OOG 1 REMARK REVDAT 3 30-AUG-23 4OOG 1 AUTHOR JRNL REMARK LINK REVDAT 2 28-MAY-14 4OOG 1 JRNL REVDAT 1 16-APR-14 4OOG 0 JRNL AUTH Y.H.LIANG,M.LAVOIE,M.A.COMEAU,S.ABOU ELELA,X.JI JRNL TITL STRUCTURE OF A EUKARYOTIC RNASE III POSTCLEAVAGE COMPLEX JRNL TITL 2 REVEALS A DOUBLE-RULER MECHANISM FOR SUBSTRATE SELECTION. JRNL REF MOL.CELL V. 54 431 2014 JRNL REFN ISSN 1097-2765 JRNL PMID 24703949 JRNL DOI 10.1016/J.MOLCEL.2014.03.006 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 31130 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1015 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 39.7236 - 4.7796 1.00 4512 160 0.1794 0.1675 REMARK 3 2 4.7796 - 3.7947 0.99 4312 156 0.1696 0.2265 REMARK 3 3 3.7947 - 3.3153 0.98 4266 137 0.2193 0.2524 REMARK 3 4 3.3153 - 3.0123 1.00 4285 158 0.2135 0.2780 REMARK 3 5 3.0123 - 2.7964 1.00 4332 113 0.2683 0.3923 REMARK 3 6 2.7964 - 2.6316 1.00 4242 156 0.3417 0.3548 REMARK 3 7 2.6316 - 2.5000 0.97 4166 135 0.4102 0.4078 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 62.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -20.72250 REMARK 3 B22 (A**2) : 42.60530 REMARK 3 B33 (A**2) : -21.88270 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 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 : 0.010 4826 REMARK 3 ANGLE : 0.777 6655 REMARK 3 CHIRALITY : 0.059 786 REMARK 3 PLANARITY : 0.003 726 REMARK 3 DIHEDRAL : 14.275 1974 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 4OOG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31418 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.78400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, REMARK 200 3O2R, 3C4T, AND 1T4O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG1000, 0.1 M TRIS-HCL, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.64450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.64450 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 78.98600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 91.90200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 78.98600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 91.90200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.64450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 78.98600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 91.90200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.64450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 78.98600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 91.90200 REMARK 290 SMTRY3 8 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 31080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -325.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 30.64450 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 A 42 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 C D 1 P C D 1 OP3 -0.127 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 TYR A 44 71.61 57.09 REMARK 500 ASP A 84 -65.18 -138.58 REMARK 500 ALA A 115 -116.78 56.39 REMARK 500 ILE A 135 -4.60 65.48 REMARK 500 TYR B 44 71.18 59.59 REMARK 500 ALA B 115 -119.75 58.51 REMARK 500 ILE B 135 -8.12 64.38 REMARK 500 LEU B 150 -70.17 -74.19 REMARK 500 ALA C 235 -62.25 -90.62 REMARK 500 HIS C 291 -115.89 46.39 REMARK 500 ASP C 302 74.55 64.06 REMARK 500 ARG C 332 -70.40 -57.74 REMARK 500 LYS C 365 -9.36 66.01 REMARK 500 ILE C 378 -59.38 -121.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE C 290 HIS C 291 129.11 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 MG C 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 238 OE1 REMARK 620 2 GLU C 241 OE1 94.1 REMARK 620 3 HOH C 705 O 87.2 83.6 REMARK 620 4 HOH C 706 O 94.6 99.2 176.6 REMARK 620 5 HOH C 707 O 100.5 165.4 97.4 79.5 REMARK 620 6 HOH C 708 O 169.9 87.1 102.9 75.3 78.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 241 OE2 REMARK 620 2 GLU C 320 OE1 101.6 REMARK 620 3 HOH C 703 O 93.3 87.1 REMARK 620 4 HOH C 704 O 81.7 75.2 160.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 245 OD2 REMARK 620 2 GLU C 320 OE2 92.8 REMARK 620 3 HOH C 701 O 76.1 95.9 REMARK 620 4 HOH C 702 O 154.9 92.6 79.0 REMARK 620 5 C D 34 O3' 86.3 178.8 83.3 88.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 27 O6 REMARK 620 2 HOH D 226 O 88.2 REMARK 620 3 HOH D 227 O 103.7 166.2 REMARK 620 4 HOH D 228 O 160.2 86.7 79.8 REMARK 620 5 HOH D 229 O 96.6 91.2 94.2 102.6 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 MG C 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NUG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIAL RNASE III COMPLEXED WITH THE PRODUCT REMARK 900 OF DSRNA PROCESSING DBREF 4OOG A 42 151 UNP Q02555 RNT1_YEAST 42 151 DBREF 4OOG B 42 151 UNP Q02555 RNT1_YEAST 42 151 DBREF 4OOG C 197 457 UNP Q02555 RNT1_YEAST 197 457 DBREF 4OOG D 1 34 PDB 4OOG 4OOG 1 34 SEQRES 1 A 110 SER ASN TYR LYS TYR LEU GLU VAL ILE GLN LEU GLU HIS SEQRES 2 A 110 ALA VAL THR LYS LEU VAL GLU SER TYR ASN LYS ILE ILE SEQRES 3 A 110 GLU LEU SER PRO ASN LEU VAL ALA TYR ASN GLU ALA VAL SEQRES 4 A 110 ASN ASN GLN ASP ARG VAL PRO VAL GLN ILE LEU PRO SER SEQRES 5 A 110 LEU SER ARG TYR GLN LEU LYS LEU ALA ALA GLU LEU LYS SEQRES 6 A 110 THR LEU HIS ASP LEU LYS LYS ASP ALA ILE LEU THR GLU SEQRES 7 A 110 ILE THR ASP TYR GLU ASN GLU PHE ASP THR GLU GLN LYS SEQRES 8 A 110 GLN PRO ILE LEU GLN GLU ILE SER LYS ALA ASP MET GLU SEQRES 9 A 110 LYS LEU GLU LYS LEU GLU SEQRES 1 B 110 SER ASN TYR LYS TYR LEU GLU VAL ILE GLN LEU GLU HIS SEQRES 2 B 110 ALA VAL THR LYS LEU VAL GLU SER TYR ASN LYS ILE ILE SEQRES 3 B 110 GLU LEU SER PRO ASN LEU VAL ALA TYR ASN GLU ALA VAL SEQRES 4 B 110 ASN ASN GLN ASP ARG VAL PRO VAL GLN ILE LEU PRO SER SEQRES 5 B 110 LEU SER ARG TYR GLN LEU LYS LEU ALA ALA GLU LEU LYS SEQRES 6 B 110 THR LEU HIS ASP LEU LYS LYS ASP ALA ILE LEU THR GLU SEQRES 7 B 110 ILE THR ASP TYR GLU ASN GLU PHE ASP THR GLU GLN LYS SEQRES 8 B 110 GLN PRO ILE LEU GLN GLU ILE SER LYS ALA ASP MET GLU SEQRES 9 B 110 LYS LEU GLU LYS LEU GLU SEQRES 1 C 261 LYS TRP PRO PRO LYS LEU PRO GLU ILE GLN ASP LEU ALA SEQRES 2 C 261 ILE ARG ALA ARG VAL PHE ILE HIS LYS SER THR ILE LYS SEQRES 3 C 261 ASP LYS VAL TYR LEU SER GLY SER GLU MET ILE ASN ALA SEQRES 4 C 261 HIS ASN GLU ARG LEU GLU PHE LEU GLY ASP SER ILE LEU SEQRES 5 C 261 ASN SER VAL MET THR LEU ILE ILE TYR ASN LYS PHE PRO SEQRES 6 C 261 ASP TYR SER GLU GLY GLN LEU SER THR LEU ARG MET ASN SEQRES 7 C 261 LEU VAL SER ASN GLU GLN ILE LYS GLN TRP SER ILE MET SEQRES 8 C 261 TYR ASN PHE HIS GLU LYS LEU LYS THR ASN PHE ASP LEU SEQRES 9 C 261 LYS ASP GLU ASN SER ASN PHE GLN ASN GLY LYS LEU LYS SEQRES 10 C 261 LEU TYR ALA ASP VAL PHE GLU ALA TYR ILE GLY GLY LEU SEQRES 11 C 261 MET GLU ASP ASP PRO ARG ASN ASN LEU PRO LYS ILE ARG SEQRES 12 C 261 LYS TRP LEU ARG LYS LEU ALA LYS PRO VAL ILE GLU GLU SEQRES 13 C 261 ALA THR ARG ASN GLN VAL ALA LEU GLU LYS THR ASP LYS SEQRES 14 C 261 LEU ASP MET ASN ALA LYS ARG GLN LEU TYR SER LEU ILE SEQRES 15 C 261 GLY TYR ALA SER LEU ARG LEU HIS TYR VAL THR VAL LYS SEQRES 16 C 261 LYS PRO THR ALA VAL ASP PRO ASN SER ILE VAL GLU CYS SEQRES 17 C 261 ARG VAL GLY ASP GLY THR VAL LEU GLY THR GLY VAL GLY SEQRES 18 C 261 ARG ASN ILE LYS ILE ALA GLY ILE ARG ALA ALA GLU ASN SEQRES 19 C 261 ALA LEU ARG ASP LYS LYS MET LEU ASP PHE TYR ALA LYS SEQRES 20 C 261 GLN ARG ALA ALA ILE PRO ARG SER GLU SER VAL LEU LYS SEQRES 21 C 261 ASP SEQRES 1 D 34 C A U G U C A U G U C A U SEQRES 2 D 34 G A G U C C A U G G C A U SEQRES 3 D 34 G G C A U G G C HET MG C 601 1 HET MG C 602 1 HET MG C 603 1 HET MG D 101 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 4(MG 2+) FORMUL 9 HOH *98(H2 O) HELIX 1 1 LYS A 45 SER A 70 1 26 HELIX 2 2 ASN A 72 ASN A 82 1 11 HELIX 3 3 PRO A 87 SER A 95 5 9 HELIX 4 4 ARG A 96 LEU A 111 1 16 HELIX 5 5 ALA A 115 PHE A 127 1 13 HELIX 6 6 ILE A 139 LEU A 150 1 12 HELIX 7 7 LYS B 45 SER B 70 1 26 HELIX 8 8 ASN B 72 ASN B 82 1 11 HELIX 9 9 PRO B 87 GLN B 89 5 3 HELIX 10 10 ILE B 90 SER B 95 1 6 HELIX 11 11 ARG B 96 LEU B 111 1 16 HELIX 12 12 ALA B 115 ASP B 122 1 8 HELIX 13 13 ASP B 122 PHE B 127 1 6 HELIX 14 14 ILE B 139 GLU B 151 1 13 HELIX 15 15 ASP C 207 VAL C 214 1 8 HELIX 16 16 HIS C 217 LYS C 222 1 6 HELIX 17 17 SER C 228 ASN C 234 1 7 HELIX 18 18 ASN C 237 PHE C 260 1 24 HELIX 19 19 SER C 264 SER C 277 1 14 HELIX 20 20 SER C 277 TYR C 288 1 12 HELIX 21 21 ASN C 289 LEU C 294 1 6 HELIX 22 22 LEU C 312 ASP C 330 1 19 HELIX 23 23 ASP C 330 GLN C 357 1 28 HELIX 24 24 VAL C 358 GLU C 361 5 4 HELIX 25 25 ASN C 369 ILE C 378 1 10 HELIX 26 26 TYR C 380 ARG C 384 5 5 HELIX 27 27 ASN C 419 ARG C 433 1 15 HELIX 28 28 ASP C 434 ALA C 447 1 14 HELIX 29 29 PRO C 449 VAL C 454 1 6 SHEET 1 A 3 HIS C 386 LYS C 391 0 SHEET 2 A 3 SER C 400 ARG C 405 -1 O ARG C 405 N HIS C 386 SHEET 3 A 3 VAL C 411 GLY C 417 -1 O LEU C 412 N CYS C 404 LINK OE1 GLU C 238 MG MG C 603 1555 1555 2.03 LINK OE2 GLU C 241 MG MG C 602 1555 1555 2.03 LINK OE1 GLU C 241 MG MG C 603 1555 1555 2.02 LINK OD2 ASP C 245 MG MG C 601 1555 1555 2.03 LINK OE2 GLU C 320 MG MG C 601 1555 1555 1.99 LINK OE1 GLU C 320 MG MG C 602 1555 1555 2.02 LINK MG MG C 601 O HOH C 701 1555 1555 2.00 LINK MG MG C 601 O HOH C 702 1555 1555 1.99 LINK MG MG C 601 O3' C D 34 1555 1555 2.00 LINK MG MG C 602 O HOH C 703 1555 1555 2.00 LINK MG MG C 602 O HOH C 704 1555 1555 2.01 LINK MG MG C 603 O HOH C 705 1555 1555 2.00 LINK MG MG C 603 O HOH C 706 1555 1555 1.99 LINK MG MG C 603 O HOH C 707 1555 1555 1.98 LINK MG MG C 603 O HOH C 708 1555 1555 2.02 LINK O6 G D 27 MG MG D 101 1555 1555 2.02 LINK MG MG D 101 O HOH D 226 1555 1555 2.01 LINK MG MG D 101 O HOH D 227 1555 1555 2.00 LINK MG MG D 101 O HOH D 228 1555 1555 2.02 LINK MG MG D 101 O HOH D 229 1555 1555 2.03 CISPEP 1 TRP C 198 PRO C 199 0 -2.13 SITE 1 AC1 7 ASP C 245 GLU C 320 MG C 602 HOH C 701 SITE 2 AC1 7 HOH C 702 C D 1 C D 34 SITE 1 AC2 6 GLU C 241 GLU C 320 MG C 601 HOH C 703 SITE 2 AC2 6 HOH C 704 C D 1 SITE 1 AC3 6 GLU C 238 GLU C 241 HOH C 705 HOH C 706 SITE 2 AC3 6 HOH C 707 HOH C 708 SITE 1 AC4 5 G D 27 HOH D 226 HOH D 227 HOH D 228 SITE 2 AC4 5 HOH D 229 CRYST1 157.972 183.804 61.289 90.00 90.00 90.00 C 2 2 21 16 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 0.006330 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016316 0.00000