HEADER HYDROLASE 09-JUL-99 1QD2 TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, TITLE 2 OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRICHOSANTHIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN, RRNA N- COMPND 5 GLYCOSIDASE, ALPHA-TCS; COMPND 6 EC: 3.2.2.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHOSANTHES KIRILOWII; SOURCE 3 ORGANISM_TAXID: 3677 KEYWDS ENZYME-PRODUCT COMPLEX OBTAINED FROM ENZYME-SUBSTRATE ANALOG COMPLEX, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.GU,Z.X.XIA REVDAT 3 14-FEB-24 1QD2 1 REMARK REVDAT 2 24-FEB-09 1QD2 1 VERSN REVDAT 1 24-APR-00 1QD2 0 JRNL AUTH Y.J.GU,Z.X.XIA JRNL TITL CRYSTAL STRUCTURES OF THE COMPLEXES OF TRICHOSANTHIN WITH JRNL TITL 2 FOUR SUBSTRATE ANALOGS AND CATALYTIC MECHANISM OF RNA JRNL TITL 3 N-GLYCOSIDASE. JRNL REF PROTEINS V. 39 37 2000 JRNL REFN ISSN 0887-3585 JRNL PMID 10737925 JRNL DOI 10.1002/(SICI)1097-0134(20000401)39:1<37::AID-PROT4>3.3.CO;2 JRNL DOI 2 -7 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 18512 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1812 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1914 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.266 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-97 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 20045 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP, CITRATE BUFFER, REMARK 280 POTASSIUM CHLORIDE, DINUCLEOTIDE APG. NATIVE CRYSTALS SOAKED IN REMARK 280 SOLUTION CONTAINING DINUCLEOTIDE APG, PH 5.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 281K 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 19.20500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.72500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.72500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.20500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.36000 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: 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 PRO A 106 20.67 -79.88 REMARK 500 TYR A 142 104.91 -45.70 REMARK 500 THR A 158 -70.63 -116.36 REMARK 500 SER A 235 18.72 -143.10 REMARK 500 ASN A 236 -71.00 -135.81 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 280 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TCS RELATED DB: PDB REMARK 900 1TCS CONTAINS THE SAME PROTEIN COMPLEXED WITH NICOTINAMIDE ADENINE REMARK 900 DINUCLEOTIDE PHOSPHATE. DBREF 1QD2 A 1 247 UNP P09989 RIPT_TRIKI 24 270 SEQRES 1 A 247 ASP VAL SER PHE ARG LEU SER GLY ALA THR SER SER SER SEQRES 2 A 247 TYR GLY VAL PHE ILE SER ASN LEU ARG LYS ALA LEU PRO SEQRES 3 A 247 ASN GLU ARG LYS LEU TYR ASP ILE PRO LEU LEU ARG SER SEQRES 4 A 247 SER LEU PRO GLY SER GLN ARG TYR ALA LEU ILE HIS LEU SEQRES 5 A 247 THR ASN TYR ALA ASP GLU THR ILE SER VAL ALA ILE ASP SEQRES 6 A 247 VAL THR ASN VAL TYR ILE MET GLY TYR ARG ALA GLY ASP SEQRES 7 A 247 THR SER TYR PHE PHE ASN GLU ALA SER ALA THR GLU ALA SEQRES 8 A 247 ALA LYS TYR VAL PHE LYS ASP ALA MET ARG LYS VAL THR SEQRES 9 A 247 LEU PRO TYR SER GLY ASN TYR GLU ARG LEU GLN THR ALA SEQRES 10 A 247 ALA GLY LYS ILE ARG GLU ASN ILE PRO LEU GLY LEU PRO SEQRES 11 A 247 ALA LEU ASP SER ALA ILE THR THR LEU PHE TYR TYR ASN SEQRES 12 A 247 ALA ASN SER ALA ALA SER ALA LEU MET VAL LEU ILE GLN SEQRES 13 A 247 SER THR SER GLU ALA ALA ARG TYR LYS PHE ILE GLU GLN SEQRES 14 A 247 GLN ILE GLY LYS ARG VAL ASP LYS THR PHE LEU PRO SER SEQRES 15 A 247 LEU ALA ILE ILE SER LEU GLU ASN SER TRP SER ALA LEU SEQRES 16 A 247 SER LYS GLN ILE GLN ILE ALA SER THR ASN ASN GLY GLN SEQRES 17 A 247 PHE GLU SER PRO VAL VAL LEU ILE ASN ALA GLN ASN GLN SEQRES 18 A 247 ARG VAL THR ILE THR ASN VAL ASP ALA GLY VAL VAL THR SEQRES 19 A 247 SER ASN ILE ALA LEU LEU LEU ASN ARG ASN ASN MET ALA HET ADE A 280 10 HETNAM ADE ADENINE FORMUL 2 ADE C5 H5 N5 FORMUL 3 HOH *189(H2 O) HELIX 1 1 THR A 10 LEU A 25 1 16 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 203 1 22 HELIX 11 11 ALA A 230 ASN A 236 1 7 HELIX 12 12 ASN A 242 MET A 246 5 5 SHEET 1 A 6 VAL A 2 ARG A 5 0 SHEET 2 A 6 TYR A 47 THR A 53 1 O LEU A 49 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 N MET A 72 O ALA A 63 SHEET 5 A 6 THR A 79 PHE A 82 -1 O THR A 79 N ALA A 76 SHEET 6 A 6 ARG A 101 THR A 104 1 O ARG A 101 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 N VAL A 223 O LEU A 215 SITE 1 AC1 8 VAL A 69 TYR A 70 ILE A 71 GLY A 109 SITE 2 AC1 8 ILE A 155 SER A 159 ARG A 163 HOH A 459 CRYST1 38.410 76.720 79.450 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 0.026035 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012587 0.00000