HEADER HYDROLASE 09-JUL-08 2K6H TITLE NMR STRUCTURE OF AN UNUSUALLY 28 KDA ACTIVE MUTANT OF MAIZE RIBOSOME- TITLE 2 INACTIVATING PROTEIN (MOD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-INACTIVATING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RRNA N-GLYCOSIDASE; COMPND 5 EC: 3.2.2.22; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_COMMON: MAIZE; SOURCE 4 ORGANISM_TAXID: 4577; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET3A KEYWDS MAIZE RIBOSOME-INACTIVATING PROTEIN, PLANT DEFENSE, PROTEIN SYNTHESIS KEYWDS 2 INHIBITOR, SOLUTION STRUCTURE, MOD, NMR SPECTROSCOPY, HYDROLASE, KEYWDS 3 TOXIN, ZYMOGEN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.YANG,A.N.MAK,P.C.SHAW,K.H.SZE REVDAT 3 16-MAR-22 2K6H 1 REMARK SEQADV REVDAT 2 16-FEB-10 2K6H 1 JRNL REVDAT 1 14-JUL-09 2K6H 0 JRNL AUTH Y.YANG,A.N.MAK,P.C.SHAW,K.H.SZE JRNL TITL SOLUTION STRUCTURE OF AN ACTIVE MUTANT OF MAIZE JRNL TITL 2 RIBOSOME-INACTIVATING PROTEIN (MOD) AND ITS INTERACTION WITH JRNL TITL 3 THE RIBOSOMAL STALK PROTEIN P2. JRNL REF J.MOL.BIOL. V. 395 897 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 19900464 JRNL DOI 10.1016/J.JMB.2009.10.051 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER REMARK 3 AUTHORS : GUNTERT, BRAUN AND WUTHRICH (CYANA), REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K6H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100736. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5MM [U-100% 13C; U-100% 15N] REMARK 210 MOD, 95% H2O/5% D2O; 1.5MM MOD, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D HBHA(CO)NH; 3D HNCACB; 3D REMARK 210 C(CO)NH; 3D HNCO; 3D HN(CO)CA; REMARK 210 3D H(CCO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNHA; 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 3D 1H-13C NOESY; 3D HCCH- REMARK 210 COSY; 3D HCCH-TOCSY-ARO; 3D 1H- REMARK 210 13C NOESY-ARO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MOLMOL, NMRPIPE REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: 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 ALA A 17 38.49 -73.06 REMARK 500 1 THR A 64 -168.92 -101.57 REMARK 500 1 HIS A 100 21.49 -74.01 REMARK 500 1 LEU A 102 23.81 -73.15 REMARK 500 1 ILE A 119 -32.65 -131.27 REMARK 500 1 LYS A 200 51.71 -93.78 REMARK 500 1 ALA A 238 -39.20 -138.09 REMARK 500 1 ALA A 246 -99.69 -79.61 REMARK 500 2 LYS A 2 62.38 -109.53 REMARK 500 2 ASN A 18 -81.44 -129.48 REMARK 500 2 PRO A 49 31.92 -65.88 REMARK 500 2 GLU A 50 106.72 53.02 REMARK 500 2 LEU A 78 71.26 30.45 REMARK 500 2 ASP A 96 55.28 38.67 REMARK 500 2 ASP A 104 -151.72 -133.27 REMARK 500 2 PRO A 106 -176.67 -69.15 REMARK 500 2 ILE A 119 -18.27 -141.42 REMARK 500 2 PRO A 150 21.43 -60.04 REMARK 500 2 ASP A 153 41.02 -84.39 REMARK 500 3 VAL A 14 -66.28 -127.17 REMARK 500 3 ASP A 104 -164.77 -74.76 REMARK 500 3 GLU A 149 84.60 -155.06 REMARK 500 3 LYS A 200 53.20 -99.96 REMARK 500 4 LEU A 78 51.68 38.83 REMARK 500 4 PHE A 93 98.50 -66.83 REMARK 500 4 ASP A 96 82.57 23.72 REMARK 500 4 LEU A 102 -2.26 69.52 REMARK 500 4 LYS A 144 88.75 -67.59 REMARK 500 4 GLU A 149 62.24 33.12 REMARK 500 4 ALA A 152 -112.51 -120.69 REMARK 500 4 THR A 245 92.89 -65.84 REMARK 500 5 LYS A 2 35.15 -72.27 REMARK 500 5 ALA A 17 43.33 -76.62 REMARK 500 5 ASN A 77 -33.57 -130.39 REMARK 500 5 TYR A 79 -102.46 -130.24 REMARK 500 5 ASP A 96 74.96 31.21 REMARK 500 5 LYS A 145 -88.27 -92.80 REMARK 500 5 VAL A 165 -79.57 -114.80 REMARK 500 5 LYS A 200 57.81 -112.63 REMARK 500 5 ASN A 242 73.07 -67.44 REMARK 500 6 ALA A 17 98.39 -66.81 REMARK 500 6 GLU A 50 91.42 -68.79 REMARK 500 6 LEU A 78 70.37 27.24 REMARK 500 6 VAL A 89 -169.54 -115.42 REMARK 500 6 ASP A 96 84.02 56.89 REMARK 500 6 LYS A 145 -43.96 128.33 REMARK 500 6 ASP A 153 2.98 -63.90 REMARK 500 7 PHE A 8 102.83 -58.36 REMARK 500 7 PRO A 13 98.17 -62.94 REMARK 500 7 ASN A 18 -67.51 -140.81 REMARK 500 REMARK 500 THIS ENTRY HAS 93 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 1 TYR A 59 0.07 SIDE CHAIN REMARK 500 1 ARG A 74 0.08 SIDE CHAIN REMARK 500 2 ARG A 170 0.08 SIDE CHAIN REMARK 500 3 TYR A 115 0.07 SIDE CHAIN REMARK 500 6 ARG A 74 0.07 SIDE CHAIN REMARK 500 7 ARG A 74 0.09 SIDE CHAIN REMARK 500 8 TYR A 19 0.08 SIDE CHAIN REMARK 500 10 ARG A 29 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2K6H A 2 147 UNP P28522 RIPX_MAIZE 17 162 DBREF 2K6H A 150 248 UNP P28522 RIPX_MAIZE 190 288 SEQADV 2K6H MET A 1 UNP P28522 EXPRESSION TAG SEQADV 2K6H LEU A 148 UNP P28522 LINKER SEQADV 2K6H GLU A 149 UNP P28522 LINKER SEQRES 1 A 248 MET LYS ARG ILE VAL PRO LYS PHE THR GLU ILE PHE PRO SEQRES 2 A 248 VAL GLU ASP ALA ASN TYR PRO TYR SER ALA PHE ILE ALA SEQRES 3 A 248 SER VAL ARG LYS ASP VAL ILE LYS HIS CYS THR ASP HIS SEQRES 4 A 248 LYS GLY ILE PHE GLN PRO VAL LEU PRO PRO GLU LYS LYS SEQRES 5 A 248 VAL PRO GLU LEU TRP LEU TYR THR GLU LEU LYS THR ARG SEQRES 6 A 248 THR SER SER ILE THR LEU ALA ILE ARG MET ASP ASN LEU SEQRES 7 A 248 TYR LEU VAL GLY PHE ARG THR PRO GLY GLY VAL TRP TRP SEQRES 8 A 248 GLU PHE GLY LYS ASP GLY ASP THR HIS LEU LEU GLY ASP SEQRES 9 A 248 ASN PRO ARG TRP LEU GLY PHE GLY GLY ARG TYR GLN ASP SEQRES 10 A 248 LEU ILE GLY ASN LYS GLY LEU GLU THR VAL THR MET GLY SEQRES 11 A 248 ARG ALA GLU MET THR ARG ALA VAL ASN ASP LEU ALA LYS SEQRES 12 A 248 LYS LYS LYS MET LEU GLU PRO GLN ALA ASP THR LYS SER SEQRES 13 A 248 LYS LEU VAL LYS LEU VAL VAL MET VAL CYS GLU GLY LEU SEQRES 14 A 248 ARG PHE ASN THR VAL SER ARG THR VAL ASP ALA GLY PHE SEQRES 15 A 248 ASN SER GLN HIS GLY VAL THR LEU THR VAL THR GLN GLY SEQRES 16 A 248 LYS GLN VAL GLN LYS TRP ASP ARG ILE SER LYS ALA ALA SEQRES 17 A 248 PHE GLU TRP ALA ASP HIS PRO THR ALA VAL ILE PRO ASP SEQRES 18 A 248 MET GLN LYS LEU GLY ILE LYS ASP LYS ASN GLU ALA ALA SEQRES 19 A 248 ARG ILE VAL ALA LEU VAL LYS ASN GLN THR THR ALA ALA SEQRES 20 A 248 ALA HELIX 1 1 PRO A 20 CYS A 36 1 17 HELIX 2 2 THR A 99 GLY A 103 5 5 HELIX 3 3 ARG A 114 ILE A 119 1 6 HELIX 4 4 GLY A 130 LYS A 143 1 14 HELIX 5 5 PRO A 150 VAL A 165 1 16 HELIX 6 6 VAL A 165 PHE A 171 1 7 HELIX 7 7 PHE A 171 ASN A 183 1 13 HELIX 8 8 THR A 191 LYS A 200 1 10 HELIX 9 9 LYS A 200 HIS A 214 1 15 HELIX 10 10 ILE A 219 LYS A 224 1 6 HELIX 11 11 ASP A 229 VAL A 237 1 9 SHEET 1 A 6 THR A 9 PRO A 13 0 SHEET 2 A 6 LEU A 58 LYS A 63 1 O GLU A 61 N PHE A 12 SHEET 3 A 6 SER A 68 ILE A 73 -1 O ILE A 73 N LEU A 58 SHEET 4 A 6 LEU A 80 THR A 85 -1 O GLY A 82 N ALA A 72 SHEET 5 A 6 VAL A 89 GLU A 92 -1 O TRP A 91 N PHE A 83 SHEET 6 A 6 ARG A 107 TRP A 108 1 O ARG A 107 N TRP A 90 SHEET 1 B 2 THR A 37 HIS A 39 0 SHEET 2 B 2 ILE A 42 VAL A 46 -1 O VAL A 46 N THR A 37 SHEET 1 C 2 THR A 128 MET A 129 0 SHEET 2 C 2 VAL A 188 THR A 189 -1 O VAL A 188 N MET A 129 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