HEADER HYDROLASE/RNA 05-AUG-13 4M30 TITLE CRYSTAL STRUCTURE OF RNASE III COMPLEXED WITH DOUBLE-STRANDED RNA AND TITLE 2 AMP (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: RNA12; 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 3 20-SEP-23 4M30 1 REMARK REVDAT 2 30-AUG-23 4M30 1 AUTHOR JRNL REMARK LINK REVDAT 1 11-DEC-13 4M30 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. 2.50 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 28395 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.480 REMARK 3 FREE R VALUE TEST SET COUNT : 988 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 29.1181 - 4.7775 0.89 3920 139 0.1922 0.2322 REMARK 3 2 4.7775 - 3.7947 0.95 4011 146 0.1640 0.2458 REMARK 3 3 3.7947 - 3.3158 0.99 4159 151 0.2026 0.2685 REMARK 3 4 3.3158 - 3.0129 1.00 4123 151 0.2194 0.2956 REMARK 3 5 3.0129 - 2.7972 0.99 4099 146 0.2480 0.3280 REMARK 3 6 2.7972 - 2.6324 0.98 4045 146 0.2667 0.3150 REMARK 3 7 2.6324 - 2.5006 0.74 3050 109 0.2707 0.3307 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 : 0.36 REMARK 3 B_SOL : 70.94 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 74.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17660 REMARK 3 B22 (A**2) : -0.17660 REMARK 3 B33 (A**2) : 0.35320 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 5117 REMARK 3 ANGLE : 1.052 7079 REMARK 3 CHIRALITY : 0.069 821 REMARK 3 PLANARITY : 0.004 679 REMARK 3 DIHEDRAL : 15.275 2115 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 4M30 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_1000081401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-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 : 28418 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 93.2 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5690 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) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.220 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 1RC7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 70% (V/V) MPD IN 0.1 M HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING 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 149.30800 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 74.65400 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 74.65400 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 149.30800 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: 10880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -171.0 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 -0.130 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 96 -86.43 -90.53 REMARK 500 ARG A 147 39.24 -90.51 REMARK 500 HIS A 179 -11.05 -40.16 REMARK 500 LYS A 181 50.64 -146.28 REMARK 500 LYS A 191 -132.17 52.55 REMARK 500 SER A 220 -71.80 -143.95 REMARK 500 ASP B 17 99.10 -168.90 REMARK 500 TYR B 30 -9.47 -173.50 REMARK 500 SER B 31 115.97 175.73 REMARK 500 LYS B 96 -103.59 -97.42 REMARK 500 HIS B 179 15.81 -56.64 REMARK 500 HIS B 180 17.81 -156.05 REMARK 500 LYS B 191 -131.04 50.86 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 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 40 OE2 REMARK 620 2 GLU A 110 OE1 99.5 REMARK 620 3 HOH A 602 O 77.4 85.9 REMARK 620 4 HOH A 603 O 78.8 92.4 155.5 REMARK 620 5 A C 103 OP2 80.8 177.2 96.9 84.9 REMARK 620 6 A C 103 OP1 154.8 104.5 96.7 107.3 75.5 REMARK 620 N 1 2 3 4 5 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 OD1 REMARK 620 2 GLU A 110 OE2 107.4 REMARK 620 3 HOH A 601 O 87.3 90.0 REMARK 620 4 A C 103 OP1 101.3 99.6 164.5 REMARK 620 5 U D 28 O3' 99.2 152.9 96.7 69.4 REMARK 620 6 HOH D 201 O 166.1 80.1 80.9 88.7 75.0 REMARK 620 N 1 2 3 4 5 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 621 O REMARK 620 2 HOH A 622 O 66.9 REMARK 620 3 HOH A 623 O 90.6 83.4 REMARK 620 4 A C 2 OP1 89.9 83.2 165.2 REMARK 620 5 HOH C 215 O 83.9 150.7 98.1 96.7 REMARK 620 6 HOH C 216 O 164.4 104.2 101.2 76.1 104.2 REMARK 620 N 1 2 3 4 5 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 A 624 O REMARK 620 2 HOH B 415 O 88.7 REMARK 620 3 A D 2 OP1 93.5 176.9 REMARK 620 4 HOH D 209 O 93.9 85.2 96.9 REMARK 620 5 HOH D 211 O 124.1 85.0 91.9 140.4 REMARK 620 6 HOH D 212 O 166.5 101.3 76.9 78.1 66.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 40 OE2 REMARK 620 2 GLU B 110 OE1 95.0 REMARK 620 3 HOH B 414 O 72.4 74.3 REMARK 620 4 A D 104 OP2 89.3 148.3 77.2 REMARK 620 5 A D 104 OP1 159.2 96.5 94.1 72.0 REMARK 620 N 1 2 3 4 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 OD1 REMARK 620 2 GLU B 110 OE2 97.1 REMARK 620 3 HOH B 401 O 78.5 99.1 REMARK 620 4 U C 28 O3' 102.7 160.1 86.8 REMARK 620 5 HOH C 218 O 158.2 89.3 79.9 73.0 REMARK 620 6 A D 104 OP1 101.0 100.4 160.4 74.1 98.3 REMARK 620 N 1 2 3 4 5 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 111.7 REMARK 620 3 HOH C 213 O 69.7 134.0 REMARK 620 4 HOH C 214 O 127.6 119.4 82.7 REMARK 620 5 HOH C 217 O 72.2 113.2 110.6 77.7 REMARK 620 N 1 2 3 4 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 91.2 REMARK 620 3 HOH D 204 O 68.7 159.5 REMARK 620 4 HOH D 210 O 81.0 100.6 81.0 REMARK 620 N 1 2 3 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 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A C 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A D 104 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: 4M2Z RELATED DB: PDB DBREF 4M30 A 1 221 UNP O67082 RNC_AQUAE 1 221 DBREF 4M30 B 1 221 UNP O67082 RNC_AQUAE 1 221 DBREF 4M30 C 2 28 PDB 4M30 4M30 2 28 DBREF 4M30 D 2 28 PDB 4M30 4M30 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 U A SEQRES 3 C 27 U 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 U A SEQRES 3 D 27 U HET MG A 501 1 HET MG A 502 1 HET MG B 301 1 HET MG B 302 1 HET MPD B 303 8 HET MG C 101 1 HET MG C 102 1 HET A C 103 23 HET MG D 101 1 HET MG D 102 1 HET MG D 103 1 HET A D 104 23 HETNAM MG MAGNESIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM A ADENOSINE-5'-MONOPHOSPHATE FORMUL 5 MG 9(MG 2+) FORMUL 9 MPD C6 H14 O2 FORMUL 12 A 2(C10 H14 N5 O7 P) FORMUL 17 HOH *70(H2 O) HELIX 1 1 MET A 3 GLY A 12 1 10 HELIX 2 2 ASP A 17 LEU A 25 1 9 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 LEU A 87 1 12 HELIX 6 6 GLU A 88 ILE A 93 5 6 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 LYS A 165 1 15 HELIX 10 10 SER A 201 GLU A 218 1 18 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 LYS B 86 1 11 HELIX 16 16 LEU B 87 ILE B 93 5 7 HELIX 17 17 ASN B 101 SER B 120 1 20 HELIX 18 18 ASP B 123 GLY B 146 1 24 HELIX 19 19 ASP B 151 LYS B 165 1 15 HELIX 20 20 SER B 201 SER B 220 1 20 SHEET 1 A 3 GLU A 169 GLU A 176 0 SHEET 2 A 3 LYS A 183 ILE A 190 -1 O ILE A 185 N ILE A 173 SHEET 3 A 3 TYR A 193 GLY A 199 -1 O GLY A 199 N PHE A 184 SHEET 1 B 3 GLU B 169 GLU B 176 0 SHEET 2 B 3 LYS B 183 ILE B 190 -1 O ILE B 185 N ILE B 173 SHEET 3 B 3 TYR B 193 GLY B 199 -1 O GLY B 199 N PHE B 184 LINK OE2 GLU A 40 MG MG A 502 1555 1555 2.05 LINK OD1 ASP A 44 MG MG A 501 1555 1555 2.01 LINK OE2 GLU A 110 MG MG A 501 1555 1555 1.98 LINK OE1 GLU A 110 MG MG A 502 1555 1555 2.08 LINK MG MG A 501 O HOH A 601 1555 1555 2.10 LINK MG MG A 501 OP1 A C 103 1555 1555 2.06 LINK MG MG A 501 O3' U D 28 1555 1555 2.07 LINK MG MG A 501 O HOH D 201 1555 1555 2.02 LINK MG MG A 502 O HOH A 602 1555 1555 2.00 LINK MG MG A 502 O HOH A 603 1555 1555 2.01 LINK MG MG A 502 OP2 A C 103 1555 1555 2.09 LINK MG MG A 502 OP1 A C 103 1555 1555 2.10 LINK O HOH A 621 MG MG C 101 1555 1555 2.04 LINK O HOH A 622 MG MG C 101 1555 1555 2.06 LINK O HOH A 623 MG MG C 101 1555 1555 2.03 LINK O HOH A 624 MG MG D 101 1555 1555 2.04 LINK OE2 GLU B 40 MG MG B 302 1555 1555 2.11 LINK OD1 ASP B 44 MG MG B 301 1555 1555 1.90 LINK OE2 GLU B 110 MG MG B 301 1555 1555 2.06 LINK OE1 GLU B 110 MG MG B 302 1555 1555 2.08 LINK MG MG B 301 O HOH B 401 1555 1555 2.11 LINK MG MG B 301 O3' U C 28 1555 1555 2.06 LINK MG MG B 301 O HOH C 218 1555 1555 1.96 LINK MG MG B 301 OP1 A D 104 1555 1555 2.03 LINK MG MG B 302 O HOH B 414 1555 1555 2.04 LINK MG MG B 302 OP2 A D 104 1555 1555 2.13 LINK MG MG B 302 OP1 A D 104 1555 1555 2.21 LINK O HOH B 415 MG MG D 101 1555 1555 2.09 LINK OP1 A C 2 MG MG C 101 1555 1555 2.02 LINK OP2 A C 2 MG MG C 102 1555 1555 2.03 LINK OP2 A C 3 MG MG C 102 1555 1555 2.03 LINK MG MG C 101 O HOH C 215 1555 1555 2.05 LINK MG MG C 101 O HOH C 216 1555 1555 2.06 LINK MG MG C 102 O HOH C 213 1555 1555 2.04 LINK MG MG C 102 O HOH C 214 1555 1555 2.07 LINK MG MG C 102 O HOH C 217 1555 1555 2.06 LINK OP1 A D 2 MG MG D 101 1555 1555 2.03 LINK OP2 A D 2 MG MG D 102 1555 1555 2.08 LINK OP2 A D 3 MG MG D 102 1555 1555 2.04 LINK MG MG D 101 O HOH D 209 1555 1555 2.00 LINK MG MG D 101 O HOH D 211 1555 1555 2.01 LINK MG MG D 101 O HOH D 212 1555 1555 2.09 LINK MG MG D 102 O HOH D 204 1555 1555 2.04 LINK MG MG D 102 O HOH D 210 1555 1555 2.14 SITE 1 AC1 7 ASP A 44 GLU A 110 MG A 502 HOH A 601 SITE 2 AC1 7 A C 103 U D 28 HOH D 201 SITE 1 AC2 6 GLU A 40 GLU A 110 MG A 501 HOH A 602 SITE 2 AC2 6 HOH A 603 A C 103 SITE 1 AC3 7 ASP B 44 GLU B 110 MG B 302 HOH B 401 SITE 2 AC3 7 U C 28 HOH C 218 A D 104 SITE 1 AC4 5 GLU B 40 GLU B 110 MG B 301 HOH B 414 SITE 2 AC4 5 A D 104 SITE 1 AC5 4 ILE A 118 VAL B 56 GLN B 57 LYS B 62 SITE 1 AC6 6 HOH A 621 HOH A 622 HOH A 623 A C 2 SITE 2 AC6 6 HOH C 215 HOH C 216 SITE 1 AC7 5 A C 2 A C 3 HOH C 213 HOH C 214 SITE 2 AC7 5 HOH C 217 SITE 1 AC8 16 GLU A 40 PHE A 41 ASP A 44 GLU A 110 SITE 2 AC8 16 MG A 501 MG A 502 HOH A 602 HOH A 603 SITE 3 AC8 16 HOH A 622 SER B 68 LYS B 71 A C 2 SITE 4 AC8 16 U C 26 A C 27 U D 28 HOH D 201 SITE 1 AC9 7 GLU A 64 HOH A 624 HOH B 415 A D 2 SITE 2 AC9 7 HOH D 209 HOH D 211 HOH D 212 SITE 1 BC1 4 A D 2 A D 3 HOH D 204 HOH D 210 SITE 1 BC2 1 C D 23 SITE 1 BC3 16 GLU A 64 SER A 68 LYS A 71 GLU B 40 SITE 2 BC3 16 PHE B 41 ASP B 44 GLU B 110 MG B 301 SITE 3 BC3 16 MG B 302 HOH B 414 U C 28 HOH C 218 SITE 4 BC3 16 A D 2 U D 26 A D 27 HOH D 211 CRYST1 81.104 81.104 223.962 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 0.012330 0.007119 0.000000 0.00000 SCALE2 0.000000 0.014237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004465 0.00000