HEADER HYDROLASE 07-JUL-11 3SRP TITLE STRUCTURE OF RIVAX: A HUMAN RICIN VACCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RICIN A CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RICIN A CHAIN, RRNA N-GLYCOSIDASE, LINKER PEPTIDE, RICIN B COMPND 5 CHAIN; COMPND 6 EC: 3.2.2.22; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS IMMUNOGEN, RIBOSOME INACTIVATING PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.M.LEGLER,C.B.MILLARD REVDAT 4 13-SEP-23 3SRP 1 REMARK SEQADV REVDAT 3 04-SEP-19 3SRP 1 SPRSDE REVDAT 2 11-JAN-12 3SRP 1 JRNL REVDAT 1 03-AUG-11 3SRP 0 SPRSDE 04-SEP-19 3SRP 3BJG JRNL AUTH P.M.LEGLER,R.N.BREY,J.E.SMALLSHAW,E.S.VITETTA,C.B.MILLARD JRNL TITL STRUCTURE OF RIVAX: A RECOMBINANT RICIN VACCINE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 826 2011 JRNL REFN ISSN 0907-4449 JRNL PMID 21904036 JRNL DOI 10.1107/S0907444911026771 REMARK 2 REMARK 2 RESOLUTION. 2.14 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 16508 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.254 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 : 2064 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 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): 0.203 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 3SRP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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 AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54188 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17463 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 68.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 12.35 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09880 REMARK 200 FOR THE DATA SET : 21.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.13 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39930 REMARK 200 FOR SHELL : 4.390 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 2AAI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% AMMONIUM SULFATE, 50 MM SODIUM REMARK 280 ACETATE PH 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 68.36000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.28000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.18000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.28000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.28000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 102.54000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.28000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.28000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.18000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.28000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.28000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.54000 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 68.36000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 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 GLU A 41 -0.34 73.18 REMARK 500 LEU A 164 -70.59 -35.41 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 SO4 A 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 269 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BJG RELATED DB: PDB REMARK 900 STRUCTURE OF RIVAX: A HUMAN RICIN VACCINE REMARK 900 RELATED ID: 3LC9 RELATED DB: PDB REMARK 900 RICIN A-CHAIN VARIANT 1-33/44-198 WITH ENGINEERED DISULFIDE BOND REMARK 900 RELATED ID: 3MK9 RELATED DB: PDB REMARK 900 STABILIZED RICIN IMMUNOGEN 1-33/44-198 DBREF 3SRP A 1 267 UNP P02879 RICI_RICCO 36 302 SEQADV 3SRP MET A 0 UNP P02879 EXPRESSION TAG SEQADV 3SRP MET A 76 UNP P02879 VAL 111 ENGINEERED MUTATION SEQADV 3SRP ALA A 80 UNP P02879 TYR 115 ENGINEERED MUTATION 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 MET THR SEQRES 7 A 268 ASN ALA ALA 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 A 268 5 HET SO4 A 269 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *144(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 SER A 155 1 16 HELIX 8 8 GLN A 160 PHE A 181 1 22 HELIX 9 9 PHE A 181 TYR A 194 1 14 HELIX 10 10 ASP A 201 GLU A 220 1 20 HELIX 11 11 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 GLY A 83 N ALA A 73 SHEET 5 A 6 SER A 89 PHE A 92 -1 O TYR A 91 N TYR A 84 SHEET 6 A 6 ASN A 113 THR A 116 1 O TYR A 115 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 4 THR A 17 GLN A 19 HIS A 65 HOH A 304 SITE 1 AC2 6 PHE A 119 GLY A 120 ASN A 122 ARG A 125 SITE 2 AC2 6 HOH A 366 HOH A 405 CRYST1 66.560 66.560 136.720 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 0.015024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007314 0.00000