HEADER HYDROLASE 23-FEB-06 2G5X TITLE CRYSTAL STRUCTURE OF LYCHNIN A TYPE 1 RIBOSOME INACTIVATING PROTEIN TITLE 2 (RIP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-INACTIVATING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYCHNIN; COMPND 5 EC: 3.2.2.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYCHNIS CHALCEDONICA; SOURCE 3 ORGANISM_COMMON: SCARLET LYCHNIS; SOURCE 4 ORGANISM_TAXID: 39855; SOURCE 5 TISSUE: SEEDS KEYWDS ALPHA-BETA PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FERMANI,G.FALINI,G.TOSI,A.RIPAMONTI,L.POLITO,A.BOLOGNESI,F.STIRPE REVDAT 4 25-OCT-23 2G5X 1 REMARK REVDAT 3 24-FEB-09 2G5X 1 VERSN REVDAT 2 13-MAR-07 2G5X 1 JRNL REVDAT 1 06-MAR-07 2G5X 0 JRNL AUTH S.FERMANI,G.FALINI,G.TOSI,A.RIPAMONTI,L.POLITO,A.BOLOGNESI, JRNL AUTH 2 F.STIRPE JRNL TITL CRYSTAL STRUCTURE OF LYCHNIN A TYPE 1 RIBOSOME INACTIVATING JRNL TITL 2 PROTEIN (RIP) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.BOLOGNESI,L.BARBIERI,A.ABBONDANZA,A.I.FALASCA, REMARK 1 AUTH 2 D.CARNICELLI,M.G.BATTELLI,F.STIRPE REMARK 1 TITL PURIFICATION AND PROPERTIES OF NEW RIBOSOME-INACTIVATING REMARK 1 TITL 2 PROTEINS WITH RNA N-GLYCOSIDASE ACTIVITY REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1087 293 1990 REMARK 1 REFN ISSN 0006-3002 REMARK 1 PMID 2248976 REMARK 1 DOI 10.1016/0167-4781(90)90002-J REMARK 1 REFERENCE 2 REMARK 1 AUTH S.FERMANI,G.FALINI,A.RIPAMONTI,A.BOLOGNESI,L.POLITO,F.STIRPE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF TWO RIBOSOME-INACTIVATING PROTEINS: LYCHNIN AND DIANTHIN REMARK 1 TITL 3 30 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 1227 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12832768 REMARK 1 DOI 10.1107/S0907444903010680 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 948638.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 21878 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) : 0.162 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2170 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2875 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 305 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1843 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.65000 REMARK 3 B22 (A**2) : -0.50000 REMARK 3 B33 (A**2) : -1.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.14000 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) : 0.06 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.09 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.640 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) : 0.980 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.350 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.680 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.46 REMARK 3 BSOL : 80.47 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: NULL REMARK 4 REMARK 4 2G5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21895 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 51.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 39.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08400 REMARK 200 FOR SHELL : 14.20 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: PDB ENTRY 1WUC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 0.1M SODIUM PHOSPHATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 28.66650 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 MONOMER. THE ASYMMETRIC UNIT CONTAIN ONE REMARK 300 MONOMER 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 VAL A 6 95.48 -59.16 REMARK 500 ASN A 41 31.57 -91.26 REMARK 500 ASP A 75 -157.71 -137.52 REMARK 500 PRO A 114 23.10 -73.26 REMARK 500 VAL A 168 -62.04 -108.42 REMARK 500 LYS A 227 99.00 -66.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RL0 RELATED DB: PDB REMARK 900 STRUCTURE OF DIANTHIN 30 REMARK 900 RELATED ID: 1WUC RELATED DB: PDB REMARK 900 STRUCTURE OF BOUGANIN DBREF 2G5X A 1 234 PDB 2G5X 2G5X 1 234 SEQRES 1 A 234 ARG PRO SER TRP THR VAL ASP SER ASP SER ALA LYS TYR SEQRES 2 A 234 SER SER PHE LEU ASP SER LEU ARG GLU GLU PHE GLY ARG SEQRES 3 A 234 GLY THR PRO LYS VAL CYS ASN ILE PRO VAL THR LYS LYS SEQRES 4 A 234 ALA ASN ASN ASP LYS PHE VAL LEU VAL ASN LEU VAL LEU SEQRES 5 A 234 PRO PHE ASN ARG ASN THR ILE THR LEU ALA PHE ARG ALA SEQRES 6 A 234 SER ASP ALA TYR LEU VAL GLY PHE GLN ASP ARG ASP SER SEQRES 7 A 234 LYS THR ASN LYS LEU ARG ALA ASN PHE PHE SER ASP GLU SEQRES 8 A 234 TYR ARG ALA LEU SER GLY LYS TYR LYS SER ILE PHE THR SEQRES 9 A 234 ASP ALA GLU VAL LEU ALA PRO ALA LEU PRO CYS ALA SER SEQRES 10 A 234 THR TYR THR ASP LEU GLN ASN LYS ALA GLY VAL SER ARG SEQRES 11 A 234 GLU LYS LEU SER LEU GLY VAL SER SER LEU GLN THR ALA SEQRES 12 A 234 PHE THR ALA VAL TYR GLY LYS VAL PHE THR GLY LYS ASN SEQRES 13 A 234 VAL ALA LYS PHE ALA LEU ILE SER ILE GLN MET VAL ALA SEQRES 14 A 234 GLU ALA ALA ARG PHE LYS TYR ILE GLU ASP GLN VAL ILE SEQRES 15 A 234 ASN ARG GLY MET TYR SER SER PHE GLU ALA GLY ALA ARG SEQRES 16 A 234 ILE THR LEU LEU GLU ASN ASN TRP SER LYS ILE SER GLU SEQRES 17 A 234 GLN TYR HIS LYS SER CYS LYS LEU GLY GLY GLY GLN PHE SEQRES 18 A 234 THR GLU GLU GLU MET LYS LEU GLY LEU LEU LEU TYR ASN FORMUL 2 HOH *364(H2 O) HELIX 1 1 ASP A 9 ARG A 26 1 18 HELIX 2 2 ALA A 40 ASP A 43 5 4 HELIX 3 3 GLU A 91 SER A 96 1 6 HELIX 4 4 LYS A 98 PHE A 103 1 6 HELIX 5 5 THR A 118 GLY A 127 1 10 HELIX 6 6 GLY A 136 ALA A 146 1 11 HELIX 7 7 THR A 153 VAL A 168 1 16 HELIX 8 8 VAL A 168 PHE A 174 1 7 HELIX 9 9 PHE A 174 GLY A 185 1 12 HELIX 10 10 ALA A 192 ASN A 202 1 11 HELIX 11 11 ASN A 202 HIS A 211 1 10 SHEET 1 A 6 SER A 3 THR A 5 0 SHEET 2 A 6 PHE A 45 VAL A 51 1 O ASN A 49 N TRP A 4 SHEET 3 A 6 THR A 58 ARG A 64 -1 O LEU A 61 N VAL A 48 SHEET 4 A 6 TYR A 69 ARG A 76 -1 O TYR A 69 N ARG A 64 SHEET 5 A 6 LEU A 83 PHE A 87 -1 O ARG A 84 N ASP A 75 SHEET 6 A 6 VAL A 108 LEU A 109 1 O VAL A 108 N ALA A 85 SSBOND 1 CYS A 32 CYS A 214 1555 1555 2.03 CRYST1 35.247 57.333 53.230 90.00 106.25 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 0.028371 0.000000 0.008271 0.00000 SCALE2 0.000000 0.017442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019568 0.00000