10 20 30 40 50 60 70 80 1RL0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE, PLANT PROTEIN 24-NOV-03 1RL0
TITLE CRYSTAL STRUCTURE OF A NEW RIBOSOME-INACTIVATING PROTEIN TITLE 2 (RIP): DIANTHIN 30
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIVIRAL PROTEIN DAP-30; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 24-278; COMPND 5 SYNONYM: RIBOSOME-INACTIVATING PROTEIN; RRNA N- COMPND 6 GLYCOSIDASE; COMPND 7 EC: 3.2.2.22
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DIANTHUS CARYOPHYLLUS; SOURCE 3 ORGANISM_COMMON: CLOVE PINK; SOURCE 4 ORGANISM_TAXID: 3570; SOURCE 5 ORGAN: LEAVES
KEYWDS MIXED BETA-SHEET, ALPHA AND BETA REGIONS, HYDROLASE, PLANT KEYWDS 2 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.FERMANI,G.FALINI,A.RIPAMONTI,A.BOLOGNESI,L.POLITO,F.STIRPE
REVDAT 3 24-FEB-09 1RL0 1 VERSN REVDAT 2 15-FEB-05 1RL0 1 JRNL REVDAT 1 07-DEC-04 1RL0 0
JRNL AUTH S.FERMANI,G.FALINI,A.RIPAMONTI,L.POLITO,F.STIRPE, JRNL AUTH 2 A.BOLOGNESI JRNL TITL THE 1.4A STRUCTURE OF DIANTHIN 30 INDICATES A ROLE JRNL TITL 2 OF SURFACE POTENTIAL AT THE ACTIVE SITE OF TYPE 1 JRNL TITL 3 RIBOSOME INACTIVATING PROTEINS JRNL REF J.STRUCT.BIOL. V. 149 204 2005 JRNL REFN ISSN 1047-8477 JRNL PMID 15681236 JRNL DOI 10.1016/J.JSB.2004.11.007
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.FERMANI,G.FALINI,A.RIPAMONTI,A.BOLOGNESI, REMARK 1 AUTH 2 L.POLITO,F.STIRPE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 ANALYSIS OF TWO RIBOSOMES-INACTIVATING PROTEINS: REMARK 1 TITL 3 LYCHNIN AND DIANTHIN 30 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 1227 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.BARBIERI,M.G.BATTELLI,F.STIRPE REMARK 1 TITL RIBOSOME-INACTIVATING PROTEINS FROM PLANTS REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1154 237 1993 REMARK 1 REFN ISSN 0006-3002 REMARK 1 REFERENCE 3 REMARK 1 AUTH F.STIRPE,D.G.WILLIAMS,L.G.ONYON,R.F.LEGG, REMARK 1 AUTH 2 W.A.STEVENS REMARK 1 TITL DIANTHINS, RIBOSOME-DAMAGING PROTEINS WITH REMARK 1 TITL 2 ANTI-VIRAL PROPERTIES FROM DIANTHUS CARYOPHYLLUS REMARK 1 TITL 3 L. (CARNATION) REMARK 1 REF BIOCHEM.J. V. 195 399 1981 REMARK 1 REFN ISSN 0264-6021
REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 916080.510 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 44520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2235 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6749 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 342 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2063 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 487 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.42000 REMARK 3 B22 (A**2) : 3.26000 REMARK 3 B33 (A**2) : -1.84000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.80000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.79 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.010 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.570 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.710 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.400 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 78.95 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD TARGET USING REMARK 3 AMPLITUDES
REMARK 4 REMARK 4 1RL0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-03. REMARK 100 THE RCSB ID CODE IS RCSB020852.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44547 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 39.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PBD ENTRY 1QI7 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM ACETATE, SODIUM REMARK 280 ACETATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K, PH 4.50
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.32700 REMARK 290 SMTRY3 2 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 300 REMARK: THE PROTEIN IS A MONOMERIC ENZYME, THE ASYMMETRIC UNIT REMARK 300 CONTAINS A SINGLE CHAIN.
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 ASP A 49 81.47 -157.39 REMARK 500 ASN A 71 -1.04 -152.89 REMARK 500 THR A 175 -78.23 -116.78 REMARK 500 ASP A 219 38.33 -145.13 REMARK 500 REMARK 500 REMARK: NULL
DBREF 1RL0 A 1 255 UNP P24476 RIP0_DIACA 24 278
SEQRES 1 A 255 ALA THR ALA TYR THR LEU ASN LEU ALA ASN PRO SER ALA SEQRES 2 A 255 SER GLN TYR SER SER PHE LEU ASP GLN ILE ARG ASN ASN SEQRES 3 A 255 VAL ARG ASP THR SER LEU ILE TYR GLY GLY THR ASP VAL SEQRES 4 A 255 ALA VAL ILE GLY ALA PRO SER THR THR ASP LYS PHE LEU SEQRES 5 A 255 ARG LEU ASN PHE GLN GLY PRO ARG GLY THR VAL SER LEU SEQRES 6 A 255 GLY LEU ARG ARG GLU ASN LEU TYR VAL VAL ALA TYR LEU SEQRES 7 A 255 ALA MET ASP ASN ALA ASN VAL ASN ARG ALA TYR TYR PHE SEQRES 8 A 255 LYS ASN GLN ILE THR SER ALA GLU LEU THR ALA LEU PHE SEQRES 9 A 255 PRO GLU VAL VAL VAL ALA ASN GLN LYS GLN LEU GLU TYR SEQRES 10 A 255 GLY GLU ASP TYR GLN ALA ILE GLU LYS ASN ALA LYS ILE SEQRES 11 A 255 THR THR GLY ASP GLN SER ARG LYS GLU LEU GLY LEU GLY SEQRES 12 A 255 ILE ASN LEU LEU ILE THR MET ILE ASP GLY VAL ASN LYS SEQRES 13 A 255 LYS VAL ARG VAL VAL LYS ASP GLU ALA ARG PHE LEU LEU SEQRES 14 A 255 ILE ALA ILE GLN MET THR ALA GLU ALA ALA ARG PHE ARG SEQRES 15 A 255 TYR ILE GLN ASN LEU VAL THR LYS ASN PHE PRO ASN LYS SEQRES 16 A 255 PHE ASP SER GLU ASN LYS VAL ILE GLN PHE GLN VAL SER SEQRES 17 A 255 TRP SER LYS ILE SER THR ALA ILE PHE GLY ASP CYS LYS SEQRES 18 A 255 ASN GLY VAL PHE ASN LYS ASP TYR ASP PHE GLY PHE GLY SEQRES 19 A 255 LYS VAL ARG GLN ALA LYS ASP LEU GLN MET GLY LEU LEU SEQRES 20 A 255 LYS TYR LEU GLY ARG PRO LYS SER
FORMUL 2 HOH *487(H2 O)
HELIX 1 1 SER A 12 ARG A 28 1 17 HELIX 2 2 THR A 96 PHE A 104 1 9 HELIX 3 3 VAL A 108 ALA A 110 5 3 HELIX 4 4 ASP A 120 ALA A 128 1 9 HELIX 5 5 SER A 136 GLY A 141 5 6 HELIX 6 6 GLY A 143 ASP A 152 1 10 HELIX 7 7 VAL A 160 THR A 175 1 16 HELIX 8 8 THR A 175 PHE A 181 1 7 HELIX 9 9 PHE A 181 ASN A 191 1 11 HELIX 10 10 GLU A 199 SER A 208 1 10 HELIX 11 11 SER A 208 ASP A 219 1 12 HELIX 12 12 LYS A 240 GLN A 243 5 4
SHEET 1 A 6 THR A 2 ASN A 7 0 SHEET 2 A 6 PHE A 51 GLY A 58 1 O ASN A 55 N LEU A 6 SHEET 3 A 6 GLY A 61 ARG A 68 -1 O VAL A 63 N PHE A 56 SHEET 4 A 6 VAL A 74 MET A 80 -1 O ALA A 76 N GLY A 66 SHEET 5 A 6 ASN A 86 TYR A 90 -1 O TYR A 89 N TYR A 77 SHEET 6 A 6 GLN A 112 GLN A 114 1 O LYS A 113 N ALA A 88 SHEET 1 B 3 CYS A 220 LYS A 221 0 SHEET 2 B 3 VAL A 224 ASP A 230 -1 O VAL A 224 N LYS A 221 SHEET 3 B 3 LYS A 235 GLN A 238 -1 O VAL A 236 N TYR A 229
CISPEP 1 PHE A 192 PRO A 193 0 -0.30
CRYST1 37.568 78.654 43.136 90.00 105.39 90.00 P 1 21 1 2
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 0.026618 0.000000 0.007327 0.00000
SCALE2 0.000000 0.012714 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024045 0.00000