HEADER HYDROLASE 15-MAR-01 1GIS TITLE A TRICHOSANTHIN(TCS) MUTANT(E85Q) COMPLEX STRUCTURE WITH 2'-DEOXY- TITLE 2 ADENOSIN-5'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.22; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHOSANTHES KIRILOWII; SOURCE 3 ORGANISM_TAXID: 3677; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-SUB COMPLEX, TRICHOSANTHIN, TCS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.GUO,Y.LIU,Y.DONG,Z.RAO REVDAT 5 29-MAY-24 1GIS 1 REMARK HET ATOM REVDAT 4 27-DEC-23 1GIS 1 REMARK REVDAT 3 10-NOV-21 1GIS 1 REMARK SEQADV SHEET REVDAT 2 24-FEB-09 1GIS 1 VERSN REVDAT 1 03-JUN-03 1GIS 0 JRNL AUTH Q.GUO,W.ZHOU,H.M.TOO,J.LI,Y.LIU,M.BARTLAM,Y.DONG,K.B.WONG, JRNL AUTH 2 P.C.SHAW,Z.RAO JRNL TITL SUBSTRATE BINDING AND CATALYSIS IN TRICHOSANTHIN OCCUR IN JRNL TITL 2 DIFFERENT SITES AS REVEALED BY THE COMPLEX STRUCTURES OF JRNL TITL 3 SEVERAL E85 MUTANTS. JRNL REF PROTEIN ENG. V. 16 391 2003 JRNL REFN ISSN 0269-2139 JRNL PMID 12874371 JRNL DOI 10.1093/PROTEIN/GZG056 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 24510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1177 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 : 1922 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 332 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.50 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.580 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: CNS REMARK 4 REMARK 4 1GIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000001561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-DEC-00 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 5.7 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24510 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 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 (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.23600 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CACL2, KCL, NAAC-HAC, PH 5.7, REMARK 280 EVAPORATION, TEMPERATURE 291.0K 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 19.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.95000 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: 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 OD1 ASP A 134 O HOH A 623 2.13 REMARK 500 O PRO A 182 O HOH A 677 2.19 REMARK 500 O ALA A 64 O HOH A 737 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 34 17.99 58.33 REMARK 500 TYR A 142 57.11 -106.05 REMARK 500 THR A 159 -72.83 -124.08 REMARK 500 ASN A 206 40.45 -142.19 REMARK 500 ASN A 237 -65.40 -128.69 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 D5M A 438 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GIU RELATED DB: PDB REMARK 900 1GIU CONTAINS TRICHOSANTHIN(TCS)(E85R) COMPLEX WITH ADENINE DBREF 1GIS A 1 248 UNP P09989 RIPT_TRIKI 23 270 SEQADV 1GIS MET A 1 UNP P09989 GLY 23 CONFLICT SEQADV 1GIS GLN A 86 UNP P09989 GLU 108 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 GLN 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 GLU 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 GLU 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 D5M A 438 22 HETNAM D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE FORMUL 2 D5M C10 H14 N5 O6 P FORMUL 3 HOH *332(H2 O) HELIX 1 1 THR A 11 LEU A 26 1 16 HELIX 2 2 PRO A 43 ARG A 47 1 5 HELIX 3 3 GLN A 86 ALA A 93 1 8 HELIX 4 5 ILE A 122 ILE A 126 5 5 HELIX 5 6 GLY A 129 TYR A 142 1 14 HELIX 6 7 SER A 147 THR A 159 1 13 HELIX 7 8 THR A 159 TYR A 165 1 7 HELIX 8 9 TYR A 165 LYS A 174 1 10 HELIX 9 10 SER A 183 THR A 205 1 23 SHEET 1 A 5 VAL A 3 ARG A 6 0 SHEET 2 A 5 TYR A 48 THR A 54 1 O LEU A 50 N VAL A 3 SHEET 3 A 5 ILE A 72 ALA A 77 -1 N MET A 73 O ALA A 64 SHEET 4 A 5 THR A 80 PHE A 83 -1 O THR A 80 N ALA A 77 SHEET 5 A 5 ARG A 102 THR A 105 1 O ARG A 102 N SER A 81 SHEET 1 B 1 ILE A 35 LEU A 38 0 SITE 1 AC1 11 TYR A 71 ILE A 72 GLN A 86 GLY A 110 SITE 2 AC1 11 ASN A 111 TYR A 112 HOH A 515 HOH A 520 SITE 3 AC1 11 HOH A 597 HOH A 640 HOH A 664 CRYST1 38.000 75.900 78.400 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 0.026316 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012755 0.00000