HEADER HYDROLASE 05-MAR-04 1SLJ TITLE SOLUTION STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: S1 DOMAIN; COMPND 5 SYNONYM: RNASE E; COMPND 6 EC: 3.1.4.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: RNE, AMS, HMP1, B1084; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS OB-FOLD, RNA-BINDING, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.SCHUBERT,R.E.EDGE,P.LARIO,M.A.COOK,N.C.J.STRYNADKA,G.A.MACKIE, AUTHOR 2 L.P.MCINTOSH REVDAT 3 02-MAR-22 1SLJ 1 REMARK SEQADV REVDAT 2 24-FEB-09 1SLJ 1 VERSN REVDAT 1 17-AUG-04 1SLJ 0 JRNL AUTH M.SCHUBERT,R.E.EDGE,P.LARIO,M.A.COOK,N.C.STRYNADKA, JRNL AUTH 2 G.A.MACKIE,L.P.MCINTOSH JRNL TITL STRUCTURAL CHARACTERIZATION OF THE RNASE E S1 DOMAIN AND JRNL TITL 2 IDENTIFICATION OF ITS OLIGONUCLEOTIDE-BINDING AND JRNL TITL 3 DIMERIZATION INTERFACES. JRNL REF J.MOL.BIOL. V. 341 37 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15312761 JRNL DOI 10.1016/J.JMB.2004.05.061 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, ARIA/CNS REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), LINGE (ARIA/CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2884 RESTRAINTS, INCLUDING REMARK 3 2113 UNAMBIGUOUS AND 597 AMBIGUOUS NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 159 DIHEDRAL ANGLE RESTRAINTS, 15 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1SLJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021813. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 75MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM RNASE E S1 U-15N,13C; 20MM REMARK 210 PHOSPHATE BUFFER; 50MM NACL; 92% REMARK 210 H2O, 8% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C_15N/13C- REMARK 210 SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY_AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4 REMARK 210 REMARK 210 REMARK: A MIXING TIME OF 100MS WAS USED. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HB2 GLU A 76 H ALA A 123 1.13 REMARK 500 HG21 ILE A 46 HD13 ILE A 49 1.27 REMARK 500 REMARK 500 REMARK: NULL 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 5 TYR A 77 CE1 TYR A 77 CZ -0.085 REMARK 500 5 TYR A 77 CZ TYR A 77 CE2 0.110 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 1 HIS A 32 68.35 -154.54 REMARK 500 1 LEU A 34 -105.16 61.81 REMARK 500 1 GLU A 35 -174.40 -173.16 REMARK 500 1 HIS A 65 141.50 63.84 REMARK 500 1 PRO A 79 141.76 -39.13 REMARK 500 1 ARG A 109 12.13 -144.10 REMARK 500 1 ASN A 111 -31.04 -130.50 REMARK 500 1 PHE A 119 46.93 -81.07 REMARK 500 1 ALA A 123 80.43 72.29 REMARK 500 2 HIS A 32 -17.70 69.85 REMARK 500 2 GLN A 36 -58.00 69.65 REMARK 500 2 LYS A 37 -17.92 -142.89 REMARK 500 2 ASN A 40 109.52 -50.66 REMARK 500 2 GLU A 54 58.01 39.87 REMARK 500 2 HIS A 65 146.77 68.59 REMARK 500 2 PRO A 79 135.45 -37.97 REMARK 500 2 ALA A 80 -7.19 -56.51 REMARK 500 2 VAL A 93 -51.91 -120.30 REMARK 500 2 GLU A 108 90.87 -66.85 REMARK 500 2 PHE A 119 47.06 -78.40 REMARK 500 2 ALA A 123 -173.89 158.34 REMARK 500 3 SER A 31 -74.33 -50.54 REMARK 500 3 LEU A 34 -94.84 -79.38 REMARK 500 3 GLU A 35 16.89 -143.94 REMARK 500 3 ASN A 40 91.57 -66.28 REMARK 500 3 HIS A 65 -159.77 61.28 REMARK 500 3 ALA A 80 -16.98 -48.99 REMARK 500 3 VAL A 93 -54.86 -121.94 REMARK 500 3 ARG A 109 18.91 -143.98 REMARK 500 3 SER A 121 19.75 -66.85 REMARK 500 3 ALA A 123 61.54 158.44 REMARK 500 4 HIS A 65 144.37 70.34 REMARK 500 4 PRO A 79 137.12 -26.72 REMARK 500 4 ARG A 109 -82.71 -105.53 REMARK 500 4 PHE A 119 44.45 -78.15 REMARK 500 4 ALA A 123 56.21 76.94 REMARK 500 5 HIS A 32 52.24 -99.26 REMARK 500 5 GLN A 36 74.02 65.35 REMARK 500 5 HIS A 65 143.28 71.25 REMARK 500 5 PRO A 79 143.65 -39.08 REMARK 500 5 ALA A 80 -7.35 -58.95 REMARK 500 5 PHE A 119 45.03 -80.25 REMARK 500 5 SER A 121 33.48 -85.03 REMARK 500 5 ALA A 123 37.67 -161.66 REMARK 500 6 HIS A 32 47.72 -152.02 REMARK 500 6 LEU A 34 -74.38 -128.48 REMARK 500 6 GLU A 54 60.23 39.23 REMARK 500 6 PRO A 79 138.02 -38.65 REMARK 500 6 VAL A 93 -54.77 -122.50 REMARK 500 6 ARG A 109 49.28 -146.65 REMARK 500 REMARK 500 THIS ENTRY HAS 83 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 TYR A 77 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SMX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI (NATIVE) REMARK 900 RELATED ID: 1SN8 RELATED DB: PDB DBREF 1SLJ A 35 125 UNP P21513 RNE_ECOLI 35 125 SEQADV 1SLJ GLY A 30 UNP P21513 CLONING ARTIFACT SEQADV 1SLJ SER A 31 UNP P21513 CLONING ARTIFACT SEQADV 1SLJ HIS A 32 UNP P21513 CLONING ARTIFACT SEQADV 1SLJ MET A 33 UNP P21513 CLONING ARTIFACT SEQADV 1SLJ LEU A 34 UNP P21513 CLONING ARTIFACT SEQRES 1 A 96 GLY SER HIS MET LEU GLU GLN LYS LYS ALA ASN ILE TYR SEQRES 2 A 96 LYS GLY LYS ILE THR ARG ILE GLU PRO SER LEU GLU ALA SEQRES 3 A 96 ALA PHE VAL ASP TYR GLY ALA GLU ARG HIS GLY PHE LEU SEQRES 4 A 96 PRO LEU LYS GLU ILE ALA ARG GLU TYR PHE PRO ALA ASN SEQRES 5 A 96 TYR SER ALA HIS GLY ARG PRO ASN ILE LYS ASP VAL LEU SEQRES 6 A 96 ARG GLU GLY GLN GLU VAL ILE VAL GLN ILE ASP LYS GLU SEQRES 7 A 96 GLU ARG GLY ASN LYS GLY ALA ALA LEU THR THR PHE ILE SEQRES 8 A 96 SER LEU ALA GLY SER HELIX 1 1 LYS A 71 ILE A 73 5 3 HELIX 2 2 ASN A 89 VAL A 93 5 5 SHEET 1 A 6 GLU A 99 VAL A 102 0 SHEET 2 A 6 TYR A 42 ILE A 49 -1 N TYR A 42 O VAL A 102 SHEET 3 A 6 ALA A 55 ASP A 59 -1 O PHE A 57 N THR A 47 SHEET 4 A 6 GLY A 66 PRO A 69 -1 O LEU A 68 N ALA A 56 SHEET 5 A 6 ALA A 114 LEU A 116 1 O ALA A 114 N PHE A 67 SHEET 6 A 6 ILE A 104 LYS A 106 -1 N LYS A 106 O ALA A 115 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1