HEADER HYDROLASE 07-JAN-03 1NLI TITLE COMPLEX OF [E160A-E189A] TRICHOSANTHIN AND ADENINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRICHOSANTHIN, RRNA N-GLYCOSIDASE, ALPHA-TCS; COMPND 5 EC: 3.2.2.22; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHOSANTHES KIRILOWII; SOURCE 3 ORGANISM_TAXID: 3677; SOURCE 4 GENE: TRICHOSANTHIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 [DE3, PLYSS]; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET8C KEYWDS PROTEIN-DNA COMPLEX, RIBOSOME-INACTIVATING PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.C.SHAW,K.B.WONG,D.S.B.CHAN,R.L.WILLIAMS REVDAT 5 16-AUG-23 1NLI 1 REMARK REVDAT 4 27-OCT-21 1NLI 1 REMARK SEQADV REVDAT 3 24-FEB-09 1NLI 1 VERSN REVDAT 2 17-JUN-03 1NLI 1 JRNL REVDAT 1 21-JAN-03 1NLI 0 JRNL AUTH P.C.SHAW,K.B.WONG,D.S.CHAN,R.L.WILLIAMS JRNL TITL STRUCTURAL BASIS FOR THE INTERACTION OF JRNL TITL 2 [E160A-E189A]-TRICHOSANTHIN WITH ADENINE. JRNL REF TOXICON V. 41 575 2003 JRNL REFN ISSN 0041-0101 JRNL PMID 12676436 JRNL DOI 10.1016/S0041-0101(02)00387-2 REMARK 2 REMARK 2 RESOLUTION. 1.93 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 16473 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 878 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.30000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : 0.58000 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 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) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1NLI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000017980. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, TRUNCATE REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16683 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 54.391 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.15500 REMARK 200 R SYM FOR SHELL (I) : 0.13200 REMARK 200 FOR SHELL : 5.400 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 1QD2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, PEG4000, MAGNESIUM CHLORIDE, REMARK 280 ADENINE HEMISULFATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K 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 18.96400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.32500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.64950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.32500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.96400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.64950 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 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: 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 ASP A 65 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 174 NE - CZ - NH1 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 174 NE - CZ - NH2 ANGL. DEV. = 9.4 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 TYR A 141 63.99 -102.87 REMARK 500 THR A 158 -82.57 -126.15 REMARK 500 ASN A 205 34.28 -140.20 REMARK 500 SER A 235 29.19 -140.35 REMARK 500 ASN A 236 -71.01 -152.97 REMARK 500 ASN A 245 37.55 -145.19 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 ADE A 248 DBREF 1NLI A 1 247 UNP P09989 RIPT_TRIKI 24 270 SEQADV 1NLI MET A 0 UNP P09989 CLONING ARTIFACT SEQADV 1NLI ALA A 160 UNP P09989 GLU 183 ENGINEERED MUTATION SEQADV 1NLI ALA A 189 UNP P09989 GLU 212 ENGINEERED MUTATION SEQRES 1 A 248 MET ASP VAL SER PHE ARG LEU SER GLY ALA THR SER SER SEQRES 2 A 248 SER TYR GLY VAL PHE ILE SER ASN LEU ARG LYS ALA LEU SEQRES 3 A 248 PRO ASN GLU ARG LYS LEU TYR ASP ILE PRO LEU LEU ARG SEQRES 4 A 248 SER SER LEU PRO GLY SER GLN ARG TYR ALA LEU ILE HIS SEQRES 5 A 248 LEU THR ASN TYR ALA ASP GLU THR ILE SER VAL ALA ILE SEQRES 6 A 248 ASP VAL THR ASN VAL TYR ILE MET GLY TYR ARG ALA GLY SEQRES 7 A 248 ASP THR SER TYR PHE PHE ASN GLU ALA SER ALA THR GLU SEQRES 8 A 248 ALA ALA LYS TYR VAL PHE LYS ASP ALA MET ARG LYS VAL SEQRES 9 A 248 THR LEU PRO TYR SER GLY ASN TYR GLU ARG LEU GLN THR SEQRES 10 A 248 ALA ALA GLY LYS ILE ARG GLU ASN ILE PRO LEU GLY LEU SEQRES 11 A 248 PRO ALA LEU ASP SER ALA ILE THR THR LEU PHE TYR TYR SEQRES 12 A 248 ASN ALA ASN SER ALA ALA SER ALA LEU MET VAL LEU ILE SEQRES 13 A 248 GLN SER THR SER ALA ALA ALA ARG TYR LYS PHE ILE GLU SEQRES 14 A 248 GLN GLN ILE GLY LYS ARG VAL ASP LYS THR PHE LEU PRO SEQRES 15 A 248 SER LEU ALA ILE ILE SER LEU ALA ASN SER TRP SER ALA SEQRES 16 A 248 LEU SER LYS GLN ILE GLN ILE ALA SER THR ASN ASN GLY SEQRES 17 A 248 GLN PHE GLU SER PRO VAL VAL LEU ILE ASN ALA GLN ASN SEQRES 18 A 248 GLN ARG VAL THR ILE THR ASN VAL ASP ALA GLY VAL VAL SEQRES 19 A 248 THR SER ASN ILE ALA LEU LEU LEU ASN ARG ASN ASN MET SEQRES 20 A 248 ALA HET ADE A 248 10 HETNAM ADE ADENINE FORMUL 2 ADE C5 H5 N5 FORMUL 3 HOH *204(H2 O) HELIX 1 1 THR A 10 ALA A 24 1 15 HELIX 2 2 PRO A 42 ARG A 46 1 5 HELIX 3 3 GLU A 85 ALA A 92 1 8 HELIX 4 4 ASN A 110 GLY A 119 1 10 HELIX 5 5 ILE A 121 ILE A 125 5 5 HELIX 6 6 GLY A 128 TYR A 141 1 14 HELIX 7 7 ASN A 143 THR A 158 1 16 HELIX 8 8 THR A 158 TYR A 164 1 7 HELIX 9 9 TYR A 164 ARG A 174 1 11 HELIX 10 10 SER A 182 SER A 191 1 10 HELIX 11 11 SER A 191 THR A 204 1 14 HELIX 12 12 ALA A 230 SER A 235 1 6 SHEET 1 A 6 VAL A 2 ARG A 5 0 SHEET 2 A 6 TYR A 47 THR A 53 1 O HIS A 51 N VAL A 2 SHEET 3 A 6 THR A 59 ASP A 65 -1 O ILE A 60 N LEU A 52 SHEET 4 A 6 ILE A 71 ALA A 76 -1 O MET A 72 N ALA A 63 SHEET 5 A 6 THR A 79 PHE A 82 -1 O TYR A 81 N TYR A 74 SHEET 6 A 6 ARG A 101 THR A 104 1 O VAL A 103 N SER A 80 SHEET 1 B 2 ASN A 27 LEU A 31 0 SHEET 2 B 2 ILE A 34 LEU A 37 -1 O ILE A 34 N LEU A 31 SHEET 1 C 2 GLN A 208 ILE A 216 0 SHEET 2 C 2 ARG A 222 ASN A 227 -1 O VAL A 223 N LEU A 215 SITE 1 AC1 9 VAL A 69 TYR A 70 ILE A 71 GLY A 109 SITE 2 AC1 9 TYR A 111 ILE A 155 SER A 159 ARG A 163 SITE 3 AC1 9 HOH A 360 CRYST1 37.928 75.299 78.650 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 0.026366 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012715 0.00000