PDB Short entry for 1I4S HEADER HYDROLASE 22-FEB-01 1I4S TITLE CRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX TITLE 2 AEOLICUS AT 2.15 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE III; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL ENDONUCLEASE DOMAIN; COMPND 5 SYNONYM: RNASE III; COMPND 6 EC: 3.1.26.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PKM803 KEYWDS RIBONUCLEASE, RNASE III, DOUBLE-STRANDED RNA, CATALYTIC DOMAIN, KEYWDS 2 ENDONUCLEASE DOMAIN, ENDONUCLEOLYTIC CLEAVAGE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BLASZCZYK,X.JI REVDAT 3 30-AUG-23 1I4S 1 AUTHOR JRNL REVDAT 2 24-FEB-09 1I4S 1 VERSN REVDAT 1 19-DEC-01 1I4S 0 JRNL AUTH J.BLASZCZYK,J.E.TROPEA,M.BUBUNENKO,K.M.ROUTZAHN,D.S.WAUGH, JRNL AUTH 2 D.L.COURT,X.JI JRNL TITL CRYSTALLOGRAPHIC AND MODELING STUDIES OF RNASE III SUGGEST A JRNL TITL 2 MECHANISM FOR DOUBLE-STRANDED RNA CLEAVAGE. JRNL REF STRUCTURE V. 9 1225 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11738048 JRNL DOI 10.1016/S0969-2126(01)00685-2 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.222 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.992 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 783 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 15686 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.208 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.168 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 718 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 13894 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2444 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2696.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9323 REMARK 3 NUMBER OF RESTRAINTS : 10091 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 ANGLE DISTANCES (A) : 0.018 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.020 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.041 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.051 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.019 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.083 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975) 201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: LEAST-SQUARES REFINEMENT USING THE REMARK 3 KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM REMARK 4 REMARK 4 1I4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98789, 1.01000, 1.03473, REMARK 200 1.04008 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16542 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.161 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.3760 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.03 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.258 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, TRIS-HCL, ACETATE, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 23.07850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.73400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.59400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.73400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.07850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.59400 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 TYR A 36 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP B 244 CB - CG - OD1 ANGL. DEV. = 6.1 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 MET A 3 -75.14 -62.08 REMARK 500 LEU A 4 -8.61 59.82 REMARK 500 LYS A 96 -92.16 -100.04 REMARK 500 LYS A 99 63.29 -152.41 REMARK 500 ASN A 101 170.39 53.09 REMARK 500 LYS B 202 60.34 -169.87 REMARK 500 MET B 203 -98.83 -122.36 REMARK 500 LEU B 204 18.79 50.25 REMARK 500 SER B 231 102.06 -178.90 REMARK 500 HIS B 235 -168.66 -114.57 REMARK 500 LYS B 262 38.83 -76.92 REMARK 500 ARG B 294 76.08 -109.50 REMARK 500 ARG B 297 31.28 75.14 REMARK 500 LYS B 299 73.50 -105.34 REMARK 500 ASN B 301 115.89 80.87 REMARK 500 THR B 303 58.20 -95.02 REMARK 500 ILE B 304 -36.38 -156.98 REMARK 500 GLU B 345 44.21 -77.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1STU RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF A DOUBLE-STRANDED RNA-BINDING DOMAIN FROM REMARK 900 DROSOPHILA STAUFEN PROTEIN REMARK 900 RELATED ID: 1DI2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DOUBLE-STRANDED RNA-BINDING DOMAIN FROM REMARK 900 XENOPUS LAEVIS COMPLEXED WITH DOUBLE-STRANDED RNA DBREF 1I4S A 1 147 UNP O67082 RNC_AQUAE 1 147 DBREF 1I4S B 201 347 UNP O67082 RNC_AQUAE 1 147 SEQRES 1 A 147 MET LYS MET LEU GLU GLN LEU GLU LYS LYS LEU GLY TYR SEQRES 2 A 147 THR PHE LYS ASP LYS SER LEU LEU GLU LYS ALA LEU THR SEQRES 3 A 147 HIS VAL SER TYR SER LYS LYS GLU HIS TYR GLU THR LEU SEQRES 4 A 147 GLU PHE LEU GLY ASP ALA LEU VAL ASN PHE PHE ILE VAL SEQRES 5 A 147 ASP LEU LEU VAL GLN TYR SER PRO ASN LYS ARG GLU GLY SEQRES 6 A 147 PHE LEU SER PRO LEU LYS ALA TYR LEU ILE SER GLU GLU SEQRES 7 A 147 PHE PHE ASN LEU LEU ALA GLN LYS LEU GLU LEU HIS LYS SEQRES 8 A 147 PHE ILE ARG ILE LYS ARG GLY LYS ILE ASN GLU THR ILE SEQRES 9 A 147 ILE GLY ASP VAL PHE GLU ALA LEU TRP ALA ALA VAL TYR SEQRES 10 A 147 ILE ASP SER GLY ARG ASP ALA ASN PHE THR ARG GLU LEU SEQRES 11 A 147 PHE TYR LYS LEU PHE LYS GLU ASP ILE LEU SER ALA ILE SEQRES 12 A 147 LYS GLU GLY ARG SEQRES 1 B 147 MET LYS MET LEU GLU GLN LEU GLU LYS LYS LEU GLY TYR SEQRES 2 B 147 THR PHE LYS ASP LYS SER LEU LEU GLU LYS ALA LEU THR SEQRES 3 B 147 HIS VAL SER TYR SER LYS LYS GLU HIS TYR GLU THR LEU SEQRES 4 B 147 GLU PHE LEU GLY ASP ALA LEU VAL ASN PHE PHE ILE VAL SEQRES 5 B 147 ASP LEU LEU VAL GLN TYR SER PRO ASN LYS ARG GLU GLY SEQRES 6 B 147 PHE LEU SER PRO LEU LYS ALA TYR LEU ILE SER GLU GLU SEQRES 7 B 147 PHE PHE ASN LEU LEU ALA GLN LYS LEU GLU LEU HIS LYS SEQRES 8 B 147 PHE ILE ARG ILE LYS ARG GLY LYS ILE ASN GLU THR ILE SEQRES 9 B 147 ILE GLY ASP VAL PHE GLU ALA LEU TRP ALA ALA VAL TYR SEQRES 10 B 147 ILE ASP SER GLY ARG ASP ALA ASN PHE THR ARG GLU LEU SEQRES 11 B 147 PHE TYR LYS LEU PHE LYS GLU ASP ILE LEU SER ALA ILE SEQRES 12 B 147 LYS GLU GLY ARG FORMUL 3 HOH *252(H2 O) HELIX 1 1 GLN A 6 GLY A 12 1 7 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 LYS A 136 1 14 HELIX 9 9 PHE A 135 GLY A 146 1 12 HELIX 10 10 GLN B 206 GLY B 212 1 7 HELIX 11 11 ASP B 217 THR B 226 1 10 HELIX 12 12 HIS B 227 SER B 231 5 5 HELIX 13 13 TYR B 236 SER B 259 1 24 HELIX 14 14 ARG B 263 ILE B 275 1 13 HELIX 15 15 SER B 276 GLN B 285 1 10 HELIX 16 16 LYS B 286 PHE B 292 5 7 HELIX 17 17 ASN B 301 SER B 320 1 20 HELIX 18 18 ASP B 323 LYS B 336 1 14 HELIX 19 19 PHE B 335 GLU B 345 1 11 CRYST1 46.157 51.188 123.468 90.00 90.00 90.00 P 21 21 21 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 0.021665 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019536 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008099 0.00000