HEADER HYDROLASE 08-JUN-99 1QI7 TITLE THE CRYSTAL STRUCTURE AT 2.0 A OF SAPORIN SO6, A RIBOSOME INACTIVATING TITLE 2 PROTEIN FROM SAPONARIA OFFICINALIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (N-GLYCOSIDASE); COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SAPONARIA OFFICINALIS; SOURCE 3 ORGANISM_COMMON: COMMON SOAPWORT; SOURCE 4 ORGANISM_TAXID: 3572; SOURCE 5 ORGAN: SEEDS; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM KEYWDS RIBOSOME INACTIVATING PROTEIN, N-GLYCOSIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.SAVINO,L.FEDERICI,R.IPPOLITI,E.LENDARO,D.TSERNOGLOU REVDAT 5 16-AUG-23 1QI7 1 REMARK REVDAT 4 04-OCT-17 1QI7 1 REMARK REVDAT 3 13-JUL-11 1QI7 1 VERSN REVDAT 2 24-FEB-09 1QI7 1 VERSN REVDAT 1 05-JUN-00 1QI7 0 JRNL AUTH C.SAVINO,L.FEDERICI,R.IPPOLITI,E.LENDARO,D.TSERNOGLOU JRNL TITL THE CRYSTAL STRUCTURE OF SAPORIN SO6 FROM SAPONARIA JRNL TITL 2 OFFICINALIS AND ITS INTERACTION WITH THE RIBOSOME. JRNL REF FEBS LETT. V. 470 239 2000 JRNL REFN ISSN 0014-5793 JRNL PMID 10745075 JRNL DOI 10.1016/S0014-5793(00)01325-9 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 19206 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2017 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; NULL REMARK 3 ANGLE DISTANCE (A) : 2.240 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000001162. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 309 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19206 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.29400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REPLACE REMARK 200 STARTING MODEL: 1PAF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.83500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.75250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.91750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.83500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 29.91750 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 89.75250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 59.83500 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 GLU A 48 OE1 - CD - OE2 ANGL. DEV. = -9.4 DEGREES REMARK 500 TYR A 72 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 VAL A 74 N - CA - CB ANGL. DEV. = -13.4 DEGREES REMARK 500 ASP A 80 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 236 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 LEU A 245 CA - CB - CG ANGL. DEV. = 16.3 DEGREES REMARK 500 MET A 247 CA - CB - CG ANGL. DEV. = 10.3 DEGREES 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 THR A 174 -73.19 -132.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 DBREF 1QI7 A 1 253 UNP P27559 RIP2_SAPOF 1 253 SEQRES 1 A 253 VAL THR SER ILE THR LEU ASP LEU VAL ASN PRO THR ALA SEQRES 2 A 253 GLY GLN TYR SER SER PHE VAL ASP LYS ILE ARG ASN ASN SEQRES 3 A 253 VAL LYS ASP PRO ASN LEU LYS TYR GLY GLY THR ASP ILE SEQRES 4 A 253 ALA VAL ILE GLY PRO PRO SER LYS GLU LYS PHE LEU ARG SEQRES 5 A 253 ILE ASN PHE GLN SER SER ARG GLY THR VAL SER LEU GLY SEQRES 6 A 253 LEU LYS ARG ASP ASN LEU TYR VAL VAL ALA TYR LEU ALA SEQRES 7 A 253 MET ASP ASN THR ASN VAL ASN ARG ALA TYR TYR PHE LYS SEQRES 8 A 253 SER GLU ILE THR SER ALA GLU LEU THR ALA LEU PHE PRO SEQRES 9 A 253 GLU ALA THR THR ALA ASN GLN LYS ALA LEU GLU TYR THR SEQRES 10 A 253 GLU ASP TYR GLN SER ILE GLU LYS ASN ALA GLN ILE THR SEQRES 11 A 253 GLN GLY ASP LYS SER ARG LYS GLU LEU GLY LEU GLY ILE SEQRES 12 A 253 ASP LEU LEU LEU THR PHE MET GLU ALA VAL ASN LYS LYS SEQRES 13 A 253 ALA ARG VAL VAL LYS ASN GLU ALA ARG PHE LEU LEU ILE SEQRES 14 A 253 ALA ILE GLN MET THR ALA GLU VAL ALA ARG PHE ARG TYR SEQRES 15 A 253 ILE GLN ASN LEU VAL THR LYS ASN PHE PRO ASN LYS PHE SEQRES 16 A 253 ASP SER ASP ASN LYS VAL ILE GLN PHE GLU VAL SER TRP SEQRES 17 A 253 ARG LYS ILE SER THR ALA ILE TYR GLY ASP ALA LYS ASN SEQRES 18 A 253 GLY VAL PHE ASN LYS ASP TYR ASP PHE GLY PHE GLY LYS SEQRES 19 A 253 VAL ARG GLN VAL LYS ASP LEU GLN MET GLY LEU LEU MET SEQRES 20 A 253 TYR LEU GLY LYS PRO LYS HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *113(H2 O) HELIX 1 1 THR A 12 LYS A 28 1 17 HELIX 2 2 THR A 95 PHE A 103 1 9 HELIX 3 3 THR A 107 ALA A 109 5 3 HELIX 4 4 ASP A 119 GLN A 128 1 10 HELIX 5 5 SER A 135 GLY A 140 5 6 HELIX 6 6 GLY A 142 ALA A 152 1 11 HELIX 7 7 VAL A 159 MET A 173 1 15 HELIX 8 8 THR A 174 PHE A 180 1 7 HELIX 9 9 PHE A 180 ASN A 190 1 11 HELIX 10 10 ASP A 198 SER A 207 1 10 HELIX 11 11 SER A 207 ASP A 218 1 12 HELIX 12 12 LYS A 239 GLN A 242 5 4 SHEET 1 A 6 THR A 2 ASP A 7 0 SHEET 2 A 6 PHE A 50 SER A 57 1 N ARG A 52 O THR A 2 SHEET 3 A 6 GLY A 60 LYS A 67 -1 N LEU A 66 O LEU A 51 SHEET 4 A 6 VAL A 73 MET A 79 -1 N LEU A 77 O SER A 63 SHEET 5 A 6 ASN A 85 TYR A 89 -1 N TYR A 88 O TYR A 76 SHEET 6 A 6 GLN A 111 ALA A 113 1 N LYS A 112 O ALA A 87 CISPEP 1 PHE A 191 PRO A 192 0 -3.33 SITE 1 AC1 5 TYR A 89 LYS A 91 THR A 95 SER A 96 SITE 2 AC1 5 ARG A 209 CRYST1 67.530 67.530 119.670 90.00 90.00 90.00 P 43 2 2 8 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 0.014808 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014808 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008356 0.00000