HEADER HYDROLASE 07-MAY-01 1IL9 TITLE STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 8-METHYL-9-OXOGUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RICIN A CHAIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.22; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RICINUS COMMUNIS; SOURCE 3 ORGANISM_COMMON: CASTOR BEAN; SOURCE 4 ORGANISM_TAXID: 3988; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURE-BASED DESIGN, TOXIN-INHIBITOR COMPLEX, GLYCOSIDASE, KEYWDS 2 HYDROLASE, RIBOSOME-INHIBITING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.J.MILLER,K.RAVIKUMAR,H.SHEN,J.-K.SUH,S.M.KERWIN,J.D.ROBERTUS REVDAT 5 13-MAR-24 1IL9 1 COMPND SOURCE REVDAT 4 16-AUG-23 1IL9 1 REMARK REVDAT 3 24-FEB-09 1IL9 1 VERSN REVDAT 2 26-DEC-06 1IL9 1 JRNL REVDAT 1 16-JAN-02 1IL9 0 JRNL AUTH D.J.MILLER,K.RAVIKUMAR,H.SHEN,J.K.SUH,S.M.KERWIN, JRNL AUTH 2 J.D.ROBERTUS JRNL TITL STRUCTURE-BASED DESIGN AND CHARACTERIZATION OF NOVEL JRNL TITL 2 PLATFORMS FOR RICIN AND SHIGA TOXIN INHIBITION. JRNL REF J.MED.CHEM. V. 45 90 2002 JRNL REFN ISSN 0022-2623 JRNL PMID 11754581 JRNL DOI 10.1021/JM010186S REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4348 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) : 0.247 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 259 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 : 2112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.210 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 1IL9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 173.0 REMARK 200 PH : 8.9 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 : DOUBLE FOCUSSING MIRRORS (NI & REMARK 200 PT) + NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5350 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 2.820 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.15920 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1RTC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, TRIS-HCL, BETA REMARK 280 -MERCAPTOETHANOL, EDTA, 8-METHYL-9-OXOGUANINE, PH 8.9, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 33.92000 REMARK 290 SMTRY3 2 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 264 CB OG 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 3 82.43 -58.59 REMARK 500 LYS A 4 127.81 70.13 REMARK 500 ALA A 14 -81.33 -115.86 REMARK 500 ALA A 16 88.33 -59.56 REMARK 500 ASP A 37 87.26 58.92 REMARK 500 GLU A 41 -31.58 73.99 REMARK 500 ASN A 78 21.79 -166.27 REMARK 500 THR A 105 47.99 -73.22 REMARK 500 HIS A 106 -25.46 -148.79 REMARK 500 TYR A 123 -56.80 -28.84 REMARK 500 THR A 159 -69.65 -104.85 REMARK 500 GLN A 160 96.07 66.25 REMARK 500 ILE A 175 -62.02 -107.80 REMARK 500 GLN A 223 27.93 41.91 REMARK 500 ILE A 251 -70.99 -93.02 REMARK 500 ARG A 258 -73.87 -105.72 REMARK 500 PRO A 262 -157.08 -69.27 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 MOG A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RTC RELATED DB: PDB REMARK 900 STRUCTURE OF RECOMBINANT RICIN A CHAIN AT 2.3 A REMARK 900 RELATED ID: 1BR6 RELATED DB: PDB REMARK 900 RICIN A CHAIN (RECOMBINANT) COMPLEX WITH PTEROIC ACID REMARK 900 RELATED ID: 1BR5 RELATED DB: PDB REMARK 900 RICIN A CHAIN (RECOMBINANT) COMPLEX WITH NEOPTERIN REMARK 900 RELATED ID: 1FMP RELATED DB: PDB REMARK 900 X-RAY ANALYSIS OF SUBSTRATE ANALOGS IN THE RICIN A-CHAIN ACTIVE SITE REMARK 900 RELATED ID: 1IL3 RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 7-DEAZAGUANINE REMARK 900 RELATED ID: 1IL4 RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 9-DEAZAGUANINE REMARK 900 RELATED ID: 1IL5 RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6- REMARK 900 DIHYDROXYPYRIMIDINE DBREF 1IL9 A 1 267 UNP P02879 RICI_RICCO 36 302 SEQRES 1 A 267 ILE PHE PRO LYS GLN TYR PRO ILE ILE ASN PHE THR THR SEQRES 2 A 267 ALA GLY ALA THR VAL GLN SER TYR THR ASN PHE ILE ARG SEQRES 3 A 267 ALA VAL ARG GLY ARG LEU THR THR GLY ALA ASP VAL ARG SEQRES 4 A 267 HIS GLU ILE PRO VAL LEU PRO ASN ARG VAL GLY LEU PRO SEQRES 5 A 267 ILE ASN GLN ARG PHE ILE LEU VAL GLU LEU SER ASN HIS SEQRES 6 A 267 ALA GLU LEU SER VAL THR LEU ALA LEU ASP VAL THR ASN SEQRES 7 A 267 ALA TYR VAL VAL GLY TYR ARG ALA GLY ASN SER ALA TYR SEQRES 8 A 267 PHE PHE HIS PRO ASP ASN GLN GLU ASP ALA GLU ALA ILE SEQRES 9 A 267 THR HIS LEU PHE THR ASP VAL GLN ASN ARG TYR THR PHE SEQRES 10 A 267 ALA PHE GLY GLY ASN TYR ASP ARG LEU GLU GLN LEU ALA SEQRES 11 A 267 GLY ASN LEU ARG GLU ASN ILE GLU LEU GLY ASN GLY PRO SEQRES 12 A 267 LEU GLU GLU ALA ILE SER ALA LEU TYR TYR TYR SER THR SEQRES 13 A 267 GLY GLY THR GLN LEU PRO THR LEU ALA ARG SER PHE ILE SEQRES 14 A 267 ILE CYS ILE GLN MET ILE SER GLU ALA ALA ARG PHE GLN SEQRES 15 A 267 TYR ILE GLU GLY GLU MET ARG THR ARG ILE ARG TYR ASN SEQRES 16 A 267 ARG ARG SER ALA PRO ASP PRO SER VAL ILE THR LEU GLU SEQRES 17 A 267 ASN SER TRP GLY ARG LEU SER THR ALA ILE GLN GLU SER SEQRES 18 A 267 ASN GLN GLY ALA PHE ALA SER PRO ILE GLN LEU GLN ARG SEQRES 19 A 267 ARG ASN GLY SER LYS PHE SER VAL TYR ASP VAL SER ILE SEQRES 20 A 267 LEU ILE PRO ILE ILE ALA LEU MET VAL TYR ARG CYS ALA SEQRES 21 A 267 PRO PRO PRO SER SER GLN PHE HET MOG A 301 12 HETNAM MOG 5-AMINO-2-METHYL-6H-OXAZOLO[5,4-D]PYRIMIDIN-7-ONE HETSYN MOG 8-METHYL-9-OXOGUANINE FORMUL 2 MOG C6 H6 N4 O2 FORMUL 3 HOH *16(H2 O) HELIX 1 1 THR A 17 THR A 33 1 17 HELIX 2 2 PRO A 52 GLN A 55 5 4 HELIX 3 3 ASN A 97 THR A 105 1 9 HELIX 4 4 ASN A 122 GLY A 131 1 10 HELIX 5 5 LEU A 133 ILE A 137 5 5 HELIX 6 6 GLY A 140 TYR A 154 1 15 HELIX 7 7 GLN A 160 PHE A 181 1 22 HELIX 8 8 PHE A 181 TYR A 194 1 14 HELIX 9 9 ASP A 201 SER A 221 1 21 HELIX 10 10 VAL A 245 ILE A 249 1 5 SHEET 1 A 6 ILE A 8 THR A 12 0 SHEET 2 A 6 PHE A 57 SER A 63 1 O LEU A 59 N ILE A 9 SHEET 3 A 6 SER A 69 ASP A 75 -1 O VAL A 70 N LEU A 62 SHEET 4 A 6 VAL A 81 ALA A 86 -1 N VAL A 82 O ALA A 73 SHEET 5 A 6 SER A 89 PHE A 92 -1 O SER A 89 N ALA A 86 SHEET 6 A 6 ASN A 113 THR A 116 1 O ASN A 113 N ALA A 90 SHEET 1 B 2 VAL A 38 ARG A 39 0 SHEET 2 B 2 ILE A 42 PRO A 43 -1 O ILE A 42 N ARG A 39 SHEET 1 C 2 ALA A 225 GLN A 233 0 SHEET 2 C 2 LYS A 239 ASP A 244 -1 O PHE A 240 N LEU A 232 SITE 1 AC1 11 ALA A 79 TYR A 80 VAL A 81 PHE A 93 SITE 2 AC1 11 GLY A 121 ASN A 122 TYR A 123 ILE A 172 SITE 3 AC1 11 SER A 176 GLU A 177 ARG A 180 CRYST1 43.040 67.840 49.680 90.00 113.26 90.00 P 1 21 1 2 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 0.023234 0.000000 0.009987 0.00000 SCALE2 0.000000 0.014741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021910 0.00000