10 20 30 40 50 60 70 80 1M58 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 09-JUL-02 1M58
TITLE SOLUTION STRUCTURE OF CYTOTOXIC RC-RNASE2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RC-RNASE2 RIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RANA CATESBEIANA; SOURCE 3 ORGANISM_COMMON: BULLFROG; SOURCE 4 ORGANISM_TAXID: 8400; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11D
KEYWDS BULLFROG, CYTOTOXICITY, RIBONUCLEASE, NMR, HYDROLASE
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR C.-H.HSU,Y.-D.LIAO,S.-H.WU,C.CHEN
REVDAT 2 24-FEB-09 1M58 1 VERSN REVDAT 1 09-JAN-03 1M58 0
JRNL AUTH C.H.HSU,L.W.CHEN,Y.D.LIAO,S.H.WU,C.CHEN JRNL TITL 1H, 15N AND 13C RESONANCE ASSIGNMENTS AND JRNL TITL 2 SECONDARY STRUCTURE DETERMINATION OF THE RC-RNASE JRNL TITL 3 2 FROM OOCYTES OF BULLFROG RANA CATESBEIANA. JRNL REF J.BIOMOL.NMR V. 19 87 2001 JRNL REFN ISSN 0925-2738 JRNL PMID 11246862 JRNL DOI 10.1023/A:1008348302036
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98 REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1M58 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUL-02. REMARK 100 THE RCSB ID CODE IS RCSB016613.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 310 REMARK 210 PH : 3.5; 3.5 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1ATM; 1ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM RRC-RNASE2 U-15N,13C; REMARK 210 50MM PHOSPHATE BUFFER; 1.5 MM REMARK 210 RRC-RNASE2 U-15N; 50MM REMARK 210 PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY, HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE, AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, AURELIA 2.6, X- REMARK 210 PLOR 98 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D REMARK 210 HETERONUCLEAR TECHNIQUES.
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 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 GLN A 2 -41.43 -131.98 REMARK 500 1 ASP A 17 50.58 -98.77 REMARK 500 1 ASP A 30 49.29 74.07 REMARK 500 1 LYS A 50 42.00 -100.51 REMARK 500 1 LYS A 73 99.90 -171.80 REMARK 500 1 LEU A 74 161.88 -43.86 REMARK 500 1 PRO A 75 -76.48 -79.02 REMARK 500 1 VAL A 97 -17.86 -140.38 REMARK 500 1 ALA A 101 -157.33 -167.33 REMARK 500 1 VAL A 102 -139.46 -109.19 REMARK 500 2 ASN A 3 -167.83 -129.83 REMARK 500 2 ASP A 17 37.03 -99.36 REMARK 500 2 ALA A 27 16.89 55.40 REMARK 500 2 LYS A 32 -173.45 -67.17 REMARK 500 2 LYS A 50 44.92 -97.77 REMARK 500 2 ASN A 51 -45.10 -141.53 REMARK 500 2 LYS A 73 107.53 177.75 REMARK 500 2 LEU A 74 169.26 -49.25 REMARK 500 2 GLU A 92 131.07 -173.56 REMARK 500 2 LYS A 94 -7.96 83.43 REMARK 500 2 ALA A 101 -163.76 -163.90 REMARK 500 2 VAL A 102 -152.19 -90.23 REMARK 500 3 ASP A 17 50.49 -91.96 REMARK 500 3 LYS A 32 -174.33 -55.67 REMARK 500 3 ASN A 51 -38.04 -132.44 REMARK 500 3 GLU A 92 132.41 -172.85 REMARK 500 3 LYS A 94 17.53 59.60 REMARK 500 3 ALA A 101 -163.56 -169.25 REMARK 500 3 VAL A 102 -141.39 -108.40 REMARK 500 4 VAL A 18 154.13 -47.76 REMARK 500 4 ASP A 30 48.19 70.17 REMARK 500 4 LYS A 32 -179.93 -66.52 REMARK 500 4 ASN A 51 26.52 -142.27 REMARK 500 4 LYS A 73 117.58 -173.24 REMARK 500 4 LEU A 74 169.35 -48.28 REMARK 500 4 ALA A 101 -163.14 -166.58 REMARK 500 4 VAL A 102 -147.25 -101.09 REMARK 500 5 ASP A 17 40.82 -97.27 REMARK 500 5 GLN A 33 -70.20 -58.46 REMARK 500 5 ALA A 40 176.74 179.51 REMARK 500 5 LYS A 50 42.55 -107.08 REMARK 500 5 ILE A 72 -47.82 -137.44 REMARK 500 5 LEU A 74 167.93 -48.18 REMARK 500 5 GLU A 92 135.10 -173.06 REMARK 500 5 VAL A 97 17.73 -150.14 REMARK 500 5 ALA A 101 -164.15 -169.37 REMARK 500 5 VAL A 102 -152.19 -92.37 REMARK 500 6 GLN A 2 -65.49 -145.82 REMARK 500 6 ASP A 17 46.42 -95.64 REMARK 500 6 LYS A 32 -172.10 -60.00 REMARK 500 6 LYS A 50 37.94 -98.28 REMARK 500 6 LYS A 73 107.11 -175.10 REMARK 500 6 LEU A 74 165.32 -49.99 REMARK 500 6 PRO A 75 -76.36 -83.61 REMARK 500 6 VAL A 97 11.14 -145.32 REMARK 500 6 ALA A 101 -162.82 -167.64 REMARK 500 6 VAL A 102 -135.44 -107.21 REMARK 500 7 ARG A 16 -44.63 -138.57 REMARK 500 7 ASP A 17 39.56 -98.29 REMARK 500 7 LYS A 50 40.69 -100.93 REMARK 500 7 ARG A 71 92.46 -62.00 REMARK 500 7 LYS A 73 116.95 -174.96 REMARK 500 7 PRO A 75 -70.15 -79.88 REMARK 500 7 VAL A 97 17.32 -148.16 REMARK 500 7 VAL A 102 -150.04 -94.77 REMARK 500 8 HIS A 11 -66.47 -100.09 REMARK 500 8 GLN A 33 -74.08 -43.94 REMARK 500 8 LYS A 73 110.64 -163.65 REMARK 500 8 LEU A 74 166.46 -45.96 REMARK 500 8 VAL A 97 -21.49 -141.98 REMARK 500 8 ALA A 101 -162.44 -163.98 REMARK 500 8 VAL A 102 -143.83 -105.30 REMARK 500 9 HIS A 11 -62.13 -96.79 REMARK 500 9 ASP A 17 44.09 -97.18 REMARK 500 9 LYS A 32 -173.22 -64.33 REMARK 500 9 LYS A 73 109.49 -176.73 REMARK 500 9 LEU A 74 170.68 -56.06 REMARK 500 9 GLU A 92 117.75 -160.26 REMARK 500 9 VAL A 100 -71.28 -83.23 REMARK 500 9 VAL A 102 -153.34 -89.14 REMARK 500 10 GLN A 33 -77.04 -56.93 REMARK 500 10 VAL A 54 -178.07 -61.85 REMARK 500 10 ILE A 72 -55.99 -142.71 REMARK 500 10 LYS A 73 117.22 -171.47 REMARK 500 10 LEU A 74 167.92 -46.78 REMARK 500 10 VAL A 102 -139.73 -104.10 REMARK 500 11 ASP A 17 34.57 -97.94 REMARK 500 11 ALA A 40 169.27 179.38 REMARK 500 11 LYS A 50 43.06 -101.89 REMARK 500 11 VAL A 54 -178.60 -64.66 REMARK 500 11 ARG A 71 98.93 -68.96 REMARK 500 11 LYS A 73 101.36 -163.80 REMARK 500 11 GLU A 92 131.57 -177.96 REMARK 500 11 VAL A 97 11.31 -143.78 REMARK 500 11 ALA A 101 -164.32 -168.16 REMARK 500 11 VAL A 102 -155.02 -94.30 REMARK 500 12 LYS A 50 46.32 -95.35 REMARK 500 12 GLU A 92 114.00 -166.72 REMARK 500 12 LYS A 94 24.42 45.23 REMARK 500 12 VAL A 100 -63.86 -91.16 REMARK 500 12 ALA A 101 -163.82 -164.85 REMARK 500 12 VAL A 102 -142.70 -105.10 REMARK 500 13 ASN A 3 -164.60 -122.11 REMARK 500 13 ASP A 17 49.29 -95.17 REMARK 500 13 ASP A 30 41.76 70.17 REMARK 500 13 LYS A 50 48.87 -97.30 REMARK 500 13 ASN A 51 -38.93 -130.15 REMARK 500 13 LYS A 73 104.22 -173.48 REMARK 500 13 ALA A 101 -161.68 -161.20 REMARK 500 13 VAL A 102 -142.06 -103.80 REMARK 500 14 ASP A 17 45.08 -100.49 REMARK 500 14 CYS A 20 -70.66 -62.96 REMARK 500 14 LYS A 50 39.98 -97.22 REMARK 500 14 LEU A 74 171.96 -50.27 REMARK 500 14 GLU A 92 125.25 -177.66 REMARK 500 14 VAL A 97 17.49 -145.96 REMARK 500 14 VAL A 102 -148.91 -96.91 REMARK 500 15 PHE A 29 -41.73 -132.72 REMARK 500 15 ASP A 30 54.07 73.92 REMARK 500 15 LYS A 50 43.88 -108.80 REMARK 500 15 LYS A 73 108.59 -165.55 REMARK 500 15 LEU A 74 167.57 -47.66 REMARK 500 15 PRO A 75 -71.76 -85.10 REMARK 500 15 GLU A 92 118.66 -164.07 REMARK 500 15 LYS A 94 14.58 59.28 REMARK 500 15 VAL A 97 13.97 -145.04 REMARK 500 15 VAL A 102 -82.85 -118.29 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 1 ARG A 16 0.25 SIDE_CHAIN REMARK 500 1 ARG A 41 0.25 SIDE_CHAIN REMARK 500 1 ARG A 44 0.32 SIDE_CHAIN REMARK 500 1 ARG A 71 0.32 SIDE_CHAIN REMARK 500 2 ARG A 16 0.32 SIDE_CHAIN REMARK 500 2 ARG A 41 0.27 SIDE_CHAIN REMARK 500 2 ARG A 44 0.31 SIDE_CHAIN REMARK 500 2 ARG A 71 0.19 SIDE_CHAIN REMARK 500 3 ARG A 16 0.26 SIDE_CHAIN REMARK 500 3 ARG A 41 0.32 SIDE_CHAIN REMARK 500 3 ARG A 44 0.32 SIDE_CHAIN REMARK 500 3 ARG A 71 0.20 SIDE_CHAIN REMARK 500 4 ARG A 16 0.21 SIDE_CHAIN REMARK 500 4 ARG A 41 0.30 SIDE_CHAIN REMARK 500 4 ARG A 44 0.28 SIDE_CHAIN REMARK 500 4 ARG A 71 0.31 SIDE_CHAIN REMARK 500 5 ARG A 16 0.24 SIDE_CHAIN REMARK 500 5 ARG A 41 0.31 SIDE_CHAIN REMARK 500 5 ARG A 44 0.30 SIDE_CHAIN REMARK 500 5 ARG A 71 0.18 SIDE_CHAIN REMARK 500 6 ARG A 16 0.20 SIDE_CHAIN REMARK 500 6 ARG A 41 0.27 SIDE_CHAIN REMARK 500 6 ARG A 44 0.28 SIDE_CHAIN REMARK 500 6 ARG A 71 0.32 SIDE_CHAIN REMARK 500 7 ARG A 16 0.31 SIDE_CHAIN REMARK 500 7 ARG A 41 0.23 SIDE_CHAIN REMARK 500 7 ARG A 44 0.22 SIDE_CHAIN REMARK 500 7 ARG A 71 0.31 SIDE_CHAIN REMARK 500 8 ARG A 16 0.26 SIDE_CHAIN REMARK 500 8 ARG A 41 0.20 SIDE_CHAIN REMARK 500 8 ARG A 44 0.29 SIDE_CHAIN REMARK 500 8 ARG A 71 0.23 SIDE_CHAIN REMARK 500 9 ARG A 16 0.29 SIDE_CHAIN REMARK 500 9 ARG A 41 0.31 SIDE_CHAIN REMARK 500 9 ARG A 44 0.23 SIDE_CHAIN REMARK 500 9 ARG A 71 0.22 SIDE_CHAIN REMARK 500 10 ARG A 16 0.23 SIDE_CHAIN REMARK 500 10 ARG A 41 0.30 SIDE_CHAIN REMARK 500 10 ARG A 44 0.23 SIDE_CHAIN REMARK 500 10 ARG A 71 0.30 SIDE_CHAIN REMARK 500 11 ARG A 16 0.31 SIDE_CHAIN REMARK 500 11 ARG A 41 0.32 SIDE_CHAIN REMARK 500 11 ARG A 44 0.22 SIDE_CHAIN REMARK 500 11 ARG A 71 0.29 SIDE_CHAIN REMARK 500 12 ARG A 16 0.19 SIDE_CHAIN REMARK 500 12 ARG A 41 0.31 SIDE_CHAIN REMARK 500 12 ARG A 44 0.31 SIDE_CHAIN REMARK 500 12 ARG A 71 0.32 SIDE_CHAIN REMARK 500 13 ARG A 16 0.29 SIDE_CHAIN REMARK 500 13 ARG A 41 0.23 SIDE_CHAIN REMARK 500 13 ARG A 44 0.31 SIDE_CHAIN REMARK 500 13 ARG A 71 0.29 SIDE_CHAIN REMARK 500 14 ARG A 16 0.30 SIDE_CHAIN REMARK 500 14 ARG A 41 0.29 SIDE_CHAIN REMARK 500 14 ARG A 44 0.30 SIDE_CHAIN REMARK 500 14 ARG A 71 0.27 SIDE_CHAIN REMARK 500 15 ARG A 16 0.29 SIDE_CHAIN REMARK 500 15 ARG A 41 0.29 SIDE_CHAIN REMARK 500 15 ARG A 44 0.26 SIDE_CHAIN REMARK 500 15 ARG A 71 0.29 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1M58 A 2 106 UNP Q9DFY8 Q9DFY8_RANCA 24 128
SEQADV 1M58 MET A 1 UNP Q9DFY8 INITIATING MET
SEQRES 1 A 106 MET GLN ASN TRP GLU THR PHE GLN LYS LYS HIS LEU THR SEQRES 2 A 106 ASP THR ARG ASP VAL LYS CYS ASP ALA GLU MET LYS LYS SEQRES 3 A 106 ALA LEU PHE ASP CYS LYS GLN LYS ASN THR PHE ILE TYR SEQRES 4 A 106 ALA ARG PRO GLY ARG VAL GLN ALA LEU CYS LYS ASN ILE SEQRES 5 A 106 ILE VAL SER LYS ASN VAL LEU SER THR ASP GLU PHE TYR SEQRES 6 A 106 LEU SER ASP CYS ASN ARG ILE LYS LEU PRO CYS HIS TYR SEQRES 7 A 106 LYS LEU LYS LYS SER SER ASN THR ILE CYS ILE THR CYS SEQRES 8 A 106 GLU ASN LYS LEU PRO VAL HIS PHE VAL ALA VAL GLU GLU SEQRES 9 A 106 CYS PRO
HELIX 1 1 ASN A 3 HIS A 11 1 9 HELIX 2 2 LYS A 19 LYS A 25 1 7 HELIX 3 3 ARG A 41 ALA A 47 1 7
SHEET 1 A 4 LEU A 12 THR A 13 0 SHEET 2 A 4 ASN A 35 TYR A 39 1 O ILE A 38 N THR A 13 SHEET 3 A 4 PHE A 64 LYS A 73 -1 O CYS A 69 N ASN A 35 SHEET 4 A 4 HIS A 77 ASN A 85 -1 O LYS A 81 N ASP A 68 SHEET 1 B 3 LYS A 56 LEU A 59 0 SHEET 2 B 3 CYS A 88 GLU A 92 -1 O ILE A 89 N VAL A 58 SHEET 3 B 3 LEU A 95 ALA A 101 -1 O ALA A 101 N CYS A 88
SSBOND 1 CYS A 20 CYS A 69 1555 1555 2.02 SSBOND 2 CYS A 31 CYS A 76 1555 1555 2.02 SSBOND 3 CYS A 49 CYS A 91 1555 1555 2.02 SSBOND 4 CYS A 88 CYS A 105 1555 1555 2.02
CISPEP 1 LEU A 74 PRO A 75 1 0.61 CISPEP 2 LEU A 74 PRO A 75 2 -0.49 CISPEP 3 LEU A 74 PRO A 75 3 -1.53 CISPEP 4 LEU A 74 PRO A 75 4 0.13 CISPEP 5 LEU A 74 PRO A 75 5 -0.15 CISPEP 6 LEU A 74 PRO A 75 6 -0.49 CISPEP 7 LEU A 74 PRO A 75 7 -0.09 CISPEP 8 LEU A 74 PRO A 75 8 -0.57 CISPEP 9 LEU A 74 PRO A 75 9 -0.17 CISPEP 10 LEU A 74 PRO A 75 10 0.41 CISPEP 11 LEU A 74 PRO A 75 11 -0.28 CISPEP 12 LEU A 74 PRO A 75 12 -0.65 CISPEP 13 LEU A 74 PRO A 75 13 0.32 CISPEP 14 LEU A 74 PRO A 75 14 -0.47 CISPEP 15 LEU A 74 PRO A 75 15 -1.19
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