HEADER HYDROLASE 14-APR-08 3CTK TITLE CRYSTAL STRUCTURE OF THE TYPE 1 RIP BOUGANIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RRNA N-GLYCOSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBOSOME INACTIVATING PROTEIN; RIP; COMPND 5 EC: 3.2.2.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOUGAINVILLEA SPECTABILIS; SOURCE 3 ORGAN: LEAVES KEYWDS ALPHA-BETA PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FERMANI,G.TOSI,G.FALINI,A.RIPAMONTI,V.FARINI,A.BOLOGNESI,L.POLITO REVDAT 6 30-OCT-24 3CTK 1 REMARK REVDAT 5 03-APR-24 3CTK 1 REMARK REVDAT 4 24-JAN-18 3CTK 1 JRNL REVDAT 3 17-NOV-09 3CTK 1 JRNL REVDAT 2 24-FEB-09 3CTK 1 VERSN REVDAT 1 27-MAY-08 3CTK 0 SPRSDE 27-MAY-08 3CTK 1WUC JRNL AUTH S.FERMANI,G.TOSI,V.FARINI,L.POLITO,G.FALINI,A.RIPAMONTI, JRNL AUTH 2 L.BARBIERI,A.CHAMBERY,A.BOLOGNESI JRNL TITL STRUCTURE/FUNCTION STUDIES ON TWO TYPE 1 RIBOSOME JRNL TITL 2 INACTIVATING PROTEINS: BOUGANIN AND LYCHNIN. JRNL REF J.STRUCT.BIOL. V. 168 278 2009 JRNL REFN ISSN 1047-8477 JRNL PMID 19616098 JRNL DOI 10.1016/J.JSB.2009.07.010 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.BOLOGNESI,L.POLITO,P.L.TAZZARI,R.L.LEMOLI,C.LUBELLI, REMARK 1 AUTH 2 M.FOGLI,L.BOON,M.DE BOER,F.STIRPE REMARK 1 TITL IN VITRO ANTI-TUMOUR ACTIVITY OF ANTI-CD80 AND ANTI-CD86 REMARK 1 TITL 2 IMMUNOTOXINS CONTAINING TYPE 1 RIBOSOME-INACTIVATING REMARK 1 TITL 3 PROTEINS REMARK 1 REF BR.J.HAEMATOL. V. 110 351 2000 REMARK 1 REFN ISSN 0007-1048 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.BOLOGNESI,L.POLITO,F.OLIVIERI,P.VALBONESI,L.BARBIERI, REMARK 1 AUTH 2 M.G.BATTELLI,M.V.CARUSI,E.BENVENUTO,F.DEL VECCHIO BLANCO, REMARK 1 AUTH 3 A.DI MARO,M.DI LORETO,F.STIRPE REMARK 1 TITL NEW RIBOSOME-INACTIVATING PROTEINS WITH REMARK 1 TITL 2 POLYNUCLEOTIDE:ADENOSINE GLYCOSIDASE AND ANTIVIRAL REMARK 1 TITL 3 ACTIVITIES FROM BASELLA RUBRA L. AND BOUGAINVILLEA REMARK 1 TITL 4 SPECTABILIS WILLD REMARK 1 REF PLANTA V. 203 422 1997 REMARK 1 REFN ISSN 0032-0935 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1593990.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23750 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) : 0.176 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1150 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3666 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE : 0.2240 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 202 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1961 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.93000 REMARK 3 B22 (A**2) : 0.82000 REMARK 3 B33 (A**2) : -1.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.110 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.680 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.070 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.110 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 60.15 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 3CTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047193. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23985 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 35.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : 0.10400 REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : 0.33000 REMARK 200 FOR SHELL : 4.400 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: PDB ENTRY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20K, PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 20.41900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.69150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.75050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.69150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.41900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.75050 REMARK 290 SMTRY3 4 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 IN SAME ASYMMETRIC UNIT 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 OXT SER A 248 O HOH A 328 2.19 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 ASP A 76 -149.66 -128.47 REMARK 500 THR A 213 -79.54 -128.36 REMARK 500 LYS A 247 159.44 134.26 REMARK 500 REMARK 500 REMARK: NULL DBREF 3CTK A 1 248 UNP Q8W4U4 Q8W4U4_9CARY 27 274 SEQRES 1 A 248 TYR ASN THR VAL SER PHE ASN LEU GLY GLU ALA TYR GLU SEQRES 2 A 248 TYR PRO THR PHE ILE GLN ASP LEU ARG ASN GLU LEU ALA SEQRES 3 A 248 LYS GLY THR PRO VAL CYS GLN LEU PRO VAL THR LEU GLN SEQRES 4 A 248 THR ILE ALA ASP ASP LYS ARG PHE VAL LEU VAL ASP ILE SEQRES 5 A 248 THR THR THR SER LYS LYS THR VAL LYS VAL ALA ILE ASP SEQRES 6 A 248 VAL THR ASP VAL TYR VAL VAL GLY TYR GLN ASP LYS TRP SEQRES 7 A 248 ASP GLY LYS ASP ARG ALA VAL PHE LEU ASP LYS VAL PRO SEQRES 8 A 248 THR VAL ALA THR SER LYS LEU PHE PRO GLY VAL THR ASN SEQRES 9 A 248 ARG VAL THR LEU THR PHE ASP GLY SER TYR GLN LYS LEU SEQRES 10 A 248 VAL ASN ALA ALA LYS VAL ASP ARG LYS ASP LEU GLU LEU SEQRES 11 A 248 GLY VAL TYR LYS LEU GLU PHE SER ILE GLU ALA ILE HIS SEQRES 12 A 248 GLY LYS THR ILE ASN GLY GLN GLU ILE ALA LYS PHE PHE SEQRES 13 A 248 LEU ILE VAL ILE GLN MET VAL SER GLU ALA ALA ARG PHE SEQRES 14 A 248 LYS TYR ILE GLU THR GLU VAL VAL ASP ARG GLY LEU TYR SEQRES 15 A 248 GLY SER PHE LYS PRO ASN PHE LYS VAL LEU ASN LEU GLU SEQRES 16 A 248 ASN ASN TRP GLY ASP ILE SER ASP ALA ILE HIS LYS SER SEQRES 17 A 248 SER PRO GLN CYS THR THR ILE ASN PRO ALA LEU GLN LEU SEQRES 18 A 248 ILE SER PRO SER ASN ASP PRO TRP VAL VAL ASN LYS VAL SEQRES 19 A 248 SER GLN ILE SER PRO ASP MET GLY ILE LEU LYS PHE LYS SEQRES 20 A 248 SER FORMUL 2 HOH *378(H2 O) HELIX 1 1 GLU A 10 TYR A 12 5 3 HELIX 2 2 GLU A 13 ALA A 26 1 14 HELIX 3 3 ALA A 42 LYS A 45 5 4 HELIX 4 4 PRO A 91 LEU A 98 1 8 HELIX 5 5 SER A 113 LYS A 122 1 10 HELIX 6 6 ASP A 124 LEU A 128 5 5 HELIX 7 7 GLY A 131 HIS A 143 1 13 HELIX 8 8 ASN A 148 VAL A 163 1 16 HELIX 9 9 VAL A 163 PHE A 169 1 7 HELIX 10 10 PHE A 169 GLY A 180 1 12 HELIX 11 11 ASN A 188 ASN A 197 1 10 HELIX 12 12 ASN A 197 SER A 209 1 13 HELIX 13 13 VAL A 234 SER A 238 1 5 HELIX 14 14 PRO A 239 MET A 241 5 3 SHEET 1 A 6 THR A 3 ASN A 7 0 SHEET 2 A 6 PHE A 47 THR A 53 1 O ASP A 51 N PHE A 6 SHEET 3 A 6 THR A 59 ASP A 65 -1 O VAL A 62 N VAL A 50 SHEET 4 A 6 VAL A 71 TRP A 78 -1 O GLY A 73 N ALA A 63 SHEET 5 A 6 LYS A 81 ASP A 88 -1 O LYS A 81 N TRP A 78 SHEET 6 A 6 ARG A 105 ASP A 111 1 O VAL A 106 N ALA A 84 SHEET 1 B 2 THR A 214 ILE A 222 0 SHEET 2 B 2 PRO A 228 LYS A 233 -1 O VAL A 231 N LEU A 219 SSBOND 1 CYS A 32 CYS A 212 1555 1555 2.04 CISPEP 1 SER A 209 PRO A 210 0 0.39 CISPEP 2 ASN A 216 PRO A 217 0 -0.03 CRYST1 40.838 77.501 79.383 90.00 90.00 90.00 P 21 21 21 4 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 0.024487 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012597 0.00000