HEADER HYDROLASE 07-APR-05 1ZB2 OBSLTE 20-NOV-07 1ZB2 2R3D TITLE RICIN A-CHAIN (RECOMBINANT) COMPLEX WITH ACETAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RICIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RICIN A-CHAIN; COMPND 5 EC: 3.2.2.22; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RICINUS COMMUNIS; SOURCE 3 ORGANISM_COMMON: CASTOR BEAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA KEYWDS RICIN, RICINUS COMMUNIS, N-GLYCOSIDASE, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR J.H.CARRA,C.A.MCHUGH,S.MULLIGAN,L.M.MACHIESKY,C.B.MILLARD REVDAT 2 20-NOV-07 1ZB2 1 OBSLTE REVDAT 1 21-MAR-06 1ZB2 0 JRNL AUTH J.H.CARRA,C.A.MCHUGH,S.MULLIGAN,L.M.MACHIESKY, JRNL AUTH 2 C.B.MILLARD JRNL TITL A CATION-PI SWITCH AT THE RICIN ACTIVE SITE JRNL TITL 2 ILLUMINATES THERMODYNAMIC CHANGES OF UREA BINDING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2064516.460 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19857 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) : 0.234 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1015 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3050 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 167 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2037 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.85000 REMARK 3 B22 (A**2) : 2.85000 REMARK 3 B33 (A**2) : -5.70000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.440 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.730 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 32.82 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : ACM.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : ACM.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZB2 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE RCSB ID CODE IS RCSB032516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-2003 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.20 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 : BRUKER NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PROTEUM R REMARK 200 DETECTOR MANUFACTURER : BRUKER NONIUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19857 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 33.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.920 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12900 REMARK 200 FOR THE DATA SET : 7.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.13 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38200 REMARK 200 FOR SHELL : 1.490 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1IFT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM ACETATE, REMARK 280 PH 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 3555 1/2-Y,1/2+X,1/4+Z REMARK 290 4555 1/2+Y,1/2-X,3/4+Z REMARK 290 5555 1/2-X,1/2+Y,1/4-Z REMARK 290 6555 1/2+X,1/2-Y,3/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.66000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.55500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.55500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.33000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.55500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.55500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.99000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.55500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.55500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.33000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.55500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.55500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.99000 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 0.00000 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 70.66000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH 409 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 0 REMARK 465 ILE A 1 REMARK 465 PHE A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 4 REMARK 465 GLN A 5 REMARK 465 SER A 264 REMARK 465 SER A 265 REMARK 465 GLN A 266 REMARK 465 PHE A 267 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 58 N - CA - C ANGL. DEV. = -7.7 DEGREES REMARK 500 ILE A 251 N - CA - C ANGL. DEV. = 7.8 DEGREES REMARK 500 VAL A 256 N - CA - C ANGL. DEV. = -7.8 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZAM RELATED DB: PDB REMARK 900 RTA COMPLEX WITH UREA REMARK 900 RELATED ID: 1ZB0 RELATED DB: PDB REMARK 900 RTA COMPLEX WITH N-METHYLUREA DBREF 1ZB2 A 1 267 UNP P02879 RICI_RICCO 36 302 SEQADV 1ZB2 MET A 0 UNP P02879 INITIATING METHIONINE SEQRES 1 A 268 MET ILE PHE PRO LYS GLN TYR PRO ILE ILE ASN PHE THR SEQRES 2 A 268 THR ALA GLY ALA THR VAL GLN SER TYR THR ASN PHE ILE SEQRES 3 A 268 ARG ALA VAL ARG GLY ARG LEU THR THR GLY ALA ASP VAL SEQRES 4 A 268 ARG HIS GLU ILE PRO VAL LEU PRO ASN ARG VAL GLY LEU SEQRES 5 A 268 PRO ILE ASN GLN ARG PHE ILE LEU VAL GLU LEU SER ASN SEQRES 6 A 268 HIS ALA GLU LEU SER VAL THR LEU ALA LEU ASP VAL THR SEQRES 7 A 268 ASN ALA TYR VAL VAL GLY TYR ARG ALA GLY ASN SER ALA SEQRES 8 A 268 TYR PHE PHE HIS PRO ASP ASN GLN GLU ASP ALA GLU ALA SEQRES 9 A 268 ILE THR HIS LEU PHE THR ASP VAL GLN ASN ARG TYR THR SEQRES 10 A 268 PHE ALA PHE GLY GLY ASN TYR ASP ARG LEU GLU GLN LEU SEQRES 11 A 268 ALA GLY ASN LEU ARG GLU ASN ILE GLU LEU GLY ASN GLY SEQRES 12 A 268 PRO LEU GLU GLU ALA ILE SER ALA LEU TYR TYR TYR SER SEQRES 13 A 268 THR GLY GLY THR GLN LEU PRO THR LEU ALA ARG SER PHE SEQRES 14 A 268 ILE ILE CYS ILE GLN MET ILE SER GLU ALA ALA ARG PHE SEQRES 15 A 268 GLN TYR ILE GLU GLY GLU MET ARG THR ARG ILE ARG TYR SEQRES 16 A 268 ASN ARG ARG SER ALA PRO ASP PRO SER VAL ILE THR LEU SEQRES 17 A 268 GLU ASN SER TRP GLY ARG LEU SER THR ALA ILE GLN GLU SEQRES 18 A 268 SER ASN GLN GLY ALA PHE ALA SER PRO ILE GLN LEU GLN SEQRES 19 A 268 ARG ARG ASN GLY SER LYS PHE SER VAL TYR ASP VAL SER SEQRES 20 A 268 ILE LEU ILE PRO ILE ILE ALA LEU MET VAL TYR ARG CYS SEQRES 21 A 268 ALA PRO PRO PRO SER SER GLN PHE HET SO4 301 5 HET SO4 302 5 HET ACM 303 4 HETNAM SO4 SULFATE ION HETNAM ACM ACETAMIDE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 ACM C2 H5 N O FORMUL 5 HOH *106(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 ILE A 104 1 8 HELIX 4 4 THR A 105 LEU A 107 5 3 HELIX 5 5 ASN A 122 GLY A 131 1 10 HELIX 6 6 LEU A 133 ILE A 137 5 5 HELIX 7 7 GLY A 140 TYR A 154 1 15 HELIX 8 8 SER A 155 GLY A 157 5 3 HELIX 9 9 GLN A 160 PHE A 181 1 22 HELIX 10 10 PHE A 181 TYR A 194 1 14 HELIX 11 11 ASP A 201 GLU A 220 1 20 HELIX 12 12 SER A 246 ILE A 249 5 4 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 O VAL A 82 N 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 TYR A 115 N PHE A 92 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 CRYST1 67.110 67.110 141.320 90.00 90.00 90.00 P 41 21 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 0.014901 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007076 0.00000