HEADER HYDROLASE/RNA 05-AUG-13 4M2Z TITLE CRYSTAL STRUCTURE OF RNASE III COMPLEXED WITH DOUBLE-STRANDED RNA AND TITLE 2 CMP (TYPE II CLEAVAGE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RIBONUCLEASE III, RNASE III; COMPND 5 EC: 3.1.26.3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA10; COMPND 9 CHAIN: C, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: AQ_946, RNC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHPK1409; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CLEAVAGE PRODUCT OF A R1.1 RNA DERIVATIVE KEYWDS RNASE III, HYDROLASE, DSRNA, RNA BINDING, RNA PROCESSING, HYDROLASE- KEYWDS 2 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.GAN,Y.-H.LIANG,G.X.SHAW,J.E.TROPEA,D.S.WAUGH,X.JI REVDAT 2 30-AUG-23 4M2Z 1 AUTHOR JRNL REMARK LINK REVDAT 1 11-DEC-13 4M2Z 0 JRNL AUTH D.L.COURT,J.GAN,Y.H.LIANG,G.X.SHAW,J.E.TROPEA,N.COSTANTINO, JRNL AUTH 2 D.S.WAUGH,X.JI JRNL TITL RNASE III: GENETICS AND FUNCTION; STRUCTURE AND MECHANISM. JRNL REF ANNU. REV. GENET. V. 47 405 2013 JRNL REFN ISSN 0066-4197 JRNL PMID 24274754 JRNL DOI 10.1146/ANNUREV-GENET-110711-155618 REMARK 2 REMARK 2 RESOLUTION. 2.85 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 18666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 857 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 29.1118 - 5.1712 0.92 3180 157 0.2070 0.2531 REMARK 3 2 5.1712 - 4.1082 0.97 3226 158 0.1779 0.2548 REMARK 3 3 4.1082 - 3.5900 0.87 2861 140 0.2564 0.3668 REMARK 3 4 3.5900 - 3.2622 0.89 2868 136 0.2836 0.3587 REMARK 3 5 3.2622 - 3.0287 0.95 3104 153 0.2621 0.3180 REMARK 3 6 3.0287 - 2.8500 0.79 2570 113 0.3119 0.3671 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 87.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 97.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 116.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.85120 REMARK 3 B22 (A**2) : 5.85120 REMARK 3 B33 (A**2) : -11.70240 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 : 0.003 5094 REMARK 3 ANGLE : 0.698 7077 REMARK 3 CHIRALITY : 0.058 820 REMARK 3 PLANARITY : 0.003 679 REMARK 3 DIHEDRAL : 14.699 2113 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 4M2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.30400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 70% (V/V) MPD IN 0.1 M HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 149.26133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.63067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 74.63067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 149.26133 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 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 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 MET B 1 REMARK 465 LYS B 2 REMARK 465 GLU B 221 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 A C 2 P A C 2 OP3 -0.127 REMARK 500 A D 2 P A D 2 OP3 -0.126 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 LYS A 33 -65.04 -101.54 REMARK 500 ARG A 163 -66.03 -94.03 REMARK 500 LYS A 191 -135.23 52.57 REMARK 500 GLU A 219 -73.37 -58.64 REMARK 500 SER A 220 -70.71 -62.87 REMARK 500 TYR B 30 -64.92 -93.24 REMARK 500 LYS B 96 -78.52 -116.90 REMARK 500 ARG B 163 -71.25 -91.79 REMARK 500 HIS B 179 -68.74 -143.37 REMARK 500 LYS B 191 -130.21 52.49 REMARK 500 GLU B 218 -64.29 -138.65 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 A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 44 OD2 REMARK 620 2 GLU A 110 OE1 101.3 REMARK 620 3 GLU A 110 OE2 121.3 47.6 REMARK 620 4 HOH A 601 O 71.6 92.7 138.4 REMARK 620 5 C C 103 OP1 84.0 120.0 78.4 142.7 REMARK 620 6 G D 28 O3' 74.8 173.1 139.2 80.7 65.7 REMARK 620 7 HOH D 205 O 136.9 100.6 100.8 70.7 115.4 79.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 606 O REMARK 620 2 A C 2 OP1 118.7 REMARK 620 3 HOH C 204 O 67.5 65.3 REMARK 620 4 HOH C 205 O 110.3 109.4 169.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 44 OD2 REMARK 620 2 ASP B 44 OD1 54.4 REMARK 620 3 GLU B 110 OE2 110.9 73.3 REMARK 620 4 HOH B 402 O 110.3 59.7 66.3 REMARK 620 5 G C 28 O3' 94.9 111.1 148.6 88.6 REMARK 620 6 C D 103 OP1 104.6 158.8 117.8 140.2 69.7 REMARK 620 7 HOH D 206 O 167.2 128.2 80.8 68.9 72.4 72.8 REMARK 620 N 1 2 3 4 5 6 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 HOH B 403 O REMARK 620 2 A D 2 OP1 149.4 REMARK 620 3 HOH D 207 O 119.9 74.7 REMARK 620 4 HOH D 208 O 94.6 92.0 132.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 2 OP2 REMARK 620 2 A C 3 OP2 87.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A D 2 OP2 REMARK 620 2 A D 3 OP2 100.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C C 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C D 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NUG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RNASE III COMPLEXED WITH DOUBLE-STRANDED RNA REMARK 900 (TYPE I CLEAVAGE) REMARK 900 RELATED ID: 4M30 RELATED DB: PDB DBREF 4M2Z A 1 221 UNP O67082 RNC_AQUAE 1 221 DBREF 4M2Z B 1 221 UNP O67082 RNC_AQUAE 1 221 DBREF 4M2Z C 2 28 PDB 4M2Z 4M2Z 2 28 DBREF 4M2Z D 2 28 PDB 4M2Z 4M2Z 2 28 SEQRES 1 A 221 MET LYS MET LEU GLU GLN LEU GLU LYS LYS LEU GLY TYR SEQRES 2 A 221 THR PHE LYS ASP LYS SER LEU LEU GLU LYS ALA LEU THR SEQRES 3 A 221 HIS VAL SER TYR SER LYS LYS GLU HIS TYR GLU THR LEU SEQRES 4 A 221 GLU PHE LEU GLY ASP ALA LEU VAL ASN PHE PHE ILE VAL SEQRES 5 A 221 ASP LEU LEU VAL GLN TYR SER PRO ASN LYS ARG GLU GLY SEQRES 6 A 221 PHE LEU SER PRO LEU LYS ALA TYR LEU ILE SER GLU GLU SEQRES 7 A 221 PHE PHE ASN LEU LEU ALA GLN LYS LEU GLU LEU HIS LYS SEQRES 8 A 221 PHE ILE ARG ILE LYS ARG GLY LYS ILE ASN GLU THR ILE SEQRES 9 A 221 ILE GLY ASP VAL PHE GLU ALA LEU TRP ALA ALA VAL TYR SEQRES 10 A 221 ILE ASP SER GLY ARG ASP ALA ASN PHE THR ARG GLU LEU SEQRES 11 A 221 PHE TYR LYS LEU PHE LYS GLU ASP ILE LEU SER ALA ILE SEQRES 12 A 221 LYS GLU GLY ARG VAL LYS LYS ASP TYR LYS THR ILE LEU SEQRES 13 A 221 GLN GLU ILE THR GLN LYS ARG TRP LYS GLU ARG PRO GLU SEQRES 14 A 221 TYR ARG LEU ILE SER VAL GLU GLY PRO HIS HIS LYS LYS SEQRES 15 A 221 LYS PHE ILE VAL GLU ALA LYS ILE LYS GLU TYR ARG THR SEQRES 16 A 221 LEU GLY GLU GLY LYS SER LYS LYS GLU ALA GLU GLN ARG SEQRES 17 A 221 ALA ALA GLU GLU LEU ILE LYS LEU LEU GLU GLU SER GLU SEQRES 1 B 221 MET LYS MET LEU GLU GLN LEU GLU LYS LYS LEU GLY TYR SEQRES 2 B 221 THR PHE LYS ASP LYS SER LEU LEU GLU LYS ALA LEU THR SEQRES 3 B 221 HIS VAL SER TYR SER LYS LYS GLU HIS TYR GLU THR LEU SEQRES 4 B 221 GLU PHE LEU GLY ASP ALA LEU VAL ASN PHE PHE ILE VAL SEQRES 5 B 221 ASP LEU LEU VAL GLN TYR SER PRO ASN LYS ARG GLU GLY SEQRES 6 B 221 PHE LEU SER PRO LEU LYS ALA TYR LEU ILE SER GLU GLU SEQRES 7 B 221 PHE PHE ASN LEU LEU ALA GLN LYS LEU GLU LEU HIS LYS SEQRES 8 B 221 PHE ILE ARG ILE LYS ARG GLY LYS ILE ASN GLU THR ILE SEQRES 9 B 221 ILE GLY ASP VAL PHE GLU ALA LEU TRP ALA ALA VAL TYR SEQRES 10 B 221 ILE ASP SER GLY ARG ASP ALA ASN PHE THR ARG GLU LEU SEQRES 11 B 221 PHE TYR LYS LEU PHE LYS GLU ASP ILE LEU SER ALA ILE SEQRES 12 B 221 LYS GLU GLY ARG VAL LYS LYS ASP TYR LYS THR ILE LEU SEQRES 13 B 221 GLN GLU ILE THR GLN LYS ARG TRP LYS GLU ARG PRO GLU SEQRES 14 B 221 TYR ARG LEU ILE SER VAL GLU GLY PRO HIS HIS LYS LYS SEQRES 15 B 221 LYS PHE ILE VAL GLU ALA LYS ILE LYS GLU TYR ARG THR SEQRES 16 B 221 LEU GLY GLU GLY LYS SER LYS LYS GLU ALA GLU GLN ARG SEQRES 17 B 221 ALA ALA GLU GLU LEU ILE LYS LEU LEU GLU GLU SER GLU SEQRES 1 C 27 A A G G U C A U U C G C A SEQRES 2 C 27 A G A G U G G C C U U G C SEQRES 3 C 27 G SEQRES 1 D 27 A A G G U C A U U C G C A SEQRES 2 D 27 A G A G U G G C C U U G C SEQRES 3 D 27 G HET MG A 501 1 HET MG B 301 1 HET MG C 101 1 HET MG C 102 1 HET C C 103 21 HET MG D 101 1 HET MG D 102 1 HET C D 103 21 HETNAM MG MAGNESIUM ION HETNAM C CYTIDINE-5'-MONOPHOSPHATE FORMUL 5 MG 6(MG 2+) FORMUL 9 C 2(C9 H14 N3 O8 P) FORMUL 13 HOH *22(H2 O) HELIX 1 1 LEU A 4 GLY A 12 1 9 HELIX 2 2 ASP A 17 THR A 26 1 10 HELIX 3 3 TYR A 36 SER A 59 1 24 HELIX 4 4 ARG A 63 ILE A 75 1 13 HELIX 5 5 SER A 76 GLU A 88 1 13 HELIX 6 6 LEU A 89 PHE A 92 5 4 HELIX 7 7 ASN A 101 SER A 120 1 20 HELIX 8 8 ASP A 123 GLU A 145 1 23 HELIX 9 9 ASP A 151 TRP A 164 1 14 HELIX 10 10 SER A 201 GLU A 221 1 21 HELIX 11 11 LEU B 4 GLY B 12 1 9 HELIX 12 12 ASP B 17 LEU B 25 1 9 HELIX 13 13 TYR B 36 SER B 59 1 24 HELIX 14 14 ARG B 63 ILE B 75 1 13 HELIX 15 15 SER B 76 GLU B 88 1 13 HELIX 16 16 LEU B 89 PHE B 92 5 4 HELIX 17 17 ASN B 101 SER B 120 1 20 HELIX 18 18 ASP B 123 GLU B 145 1 23 HELIX 19 19 ASP B 151 TRP B 164 1 14 HELIX 20 20 SER B 201 LEU B 217 1 17 SHEET 1 A 3 GLU A 169 GLU A 176 0 SHEET 2 A 3 LYS A 183 ILE A 190 -1 O GLU A 187 N ARG A 171 SHEET 3 A 3 TYR A 193 THR A 195 -1 O TYR A 193 N ILE A 190 SHEET 1 B 3 GLU A 169 GLU A 176 0 SHEET 2 B 3 LYS A 183 ILE A 190 -1 O GLU A 187 N ARG A 171 SHEET 3 B 3 GLU A 198 GLY A 199 -1 O GLY A 199 N PHE A 184 SHEET 1 C 3 GLU B 169 GLU B 176 0 SHEET 2 C 3 LYS B 183 ILE B 190 -1 O LYS B 183 N GLU B 176 SHEET 3 C 3 TYR B 193 GLY B 199 -1 O TYR B 193 N ILE B 190 LINK OD2 ASP A 44 MG MG A 501 1555 1555 1.99 LINK OE1 GLU A 110 MG MG A 501 1555 1555 2.09 LINK OE2 GLU A 110 MG MG A 501 1555 1555 2.95 LINK MG MG A 501 O HOH A 601 1555 1555 1.99 LINK MG MG A 501 OP1 C C 103 1555 1555 1.98 LINK MG MG A 501 O3' G D 28 1555 1555 2.10 LINK MG MG A 501 O HOH D 205 1555 1555 2.00 LINK O HOH A 606 MG MG C 101 1555 1555 2.07 LINK OD2 ASP B 44 MG MG B 301 1555 1555 2.01 LINK OD1 ASP B 44 MG MG B 301 1555 1555 2.63 LINK OE2 GLU B 110 MG MG B 301 1555 1555 2.03 LINK MG MG B 301 O HOH B 402 1555 1555 2.03 LINK MG MG B 301 O3' G C 28 1555 1555 2.04 LINK MG MG B 301 OP1 C D 103 1555 1555 1.99 LINK MG MG B 301 O HOH D 206 1555 1555 2.02 LINK O HOH B 403 MG MG D 101 1555 1555 2.00 LINK OP1 A C 2 MG MG C 101 1555 1555 2.00 LINK OP2 A C 2 MG MG C 102 1555 1555 2.01 LINK OP2 A C 3 MG MG C 102 1555 1555 2.01 LINK MG MG C 101 O HOH C 204 1555 1555 2.14 LINK MG MG C 101 O HOH C 205 1555 1555 2.02 LINK OP1 A D 2 MG MG D 101 1555 1555 2.00 LINK OP2 A D 2 MG MG D 102 1555 1555 2.01 LINK OP2 A D 3 MG MG D 102 1555 1555 2.01 LINK MG MG D 101 O HOH D 207 1555 1555 2.01 LINK MG MG D 101 O HOH D 208 1555 1555 2.01 SITE 1 AC1 6 ASP A 44 GLU A 110 HOH A 601 C C 103 SITE 2 AC1 6 G D 28 HOH D 205 SITE 1 AC2 6 ASP B 44 GLU B 110 HOH B 402 G C 28 SITE 2 AC2 6 C D 103 HOH D 206 SITE 1 AC3 5 HOH A 606 GLU B 64 A C 2 HOH C 204 SITE 2 AC3 5 HOH C 205 SITE 1 AC4 2 A C 2 A C 3 SITE 1 AC5 13 GLU A 40 PHE A 41 ASP A 44 GLU A 110 SITE 2 AC5 13 MG A 501 GLU B 64 SER B 68 LYS B 71 SITE 3 AC5 13 A C 2 G C 26 C C 27 HOH C 204 SITE 4 AC5 13 G D 28 SITE 1 AC6 5 GLU A 64 HOH B 403 A D 2 HOH D 207 SITE 2 AC6 5 HOH D 208 SITE 1 AC7 2 A D 2 A D 3 SITE 1 AC8 14 GLU A 64 SER A 68 LYS A 71 GLU B 40 SITE 2 AC8 14 PHE B 41 ASP B 44 GLU B 110 MG B 301 SITE 3 AC8 14 G C 28 A D 2 G D 26 C D 27 SITE 4 AC8 14 HOH D 206 HOH D 207 CRYST1 81.131 81.131 223.892 90.00 90.00 120.00 P 32 2 1 12 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 0.012326 0.007116 0.000000 0.00000 SCALE2 0.000000 0.014233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004466 0.00000