PDB Short entry for 4HV3 HEADER HYDROLASE/HYDROLASE INHIBITOR 05-NOV-12 4HV3 TITLE STRUCTURE OF RICIN A CHAIN BOUND WITH N-(N-(PTERIN-7-YL)CARBONYL-L- TITLE 2 SERINYL)-L-TRYPTOPHAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RICIN; 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 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; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM101; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUTA KEYWDS RICIN, PROTEIN-LIGAND COMPLEX, PTERIN, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX, TOXIN, HYDROLASE, RIBOSOME-INACTIVATING PROTEIN, N- KEYWDS 3 GLYCOSIDASE EXPDTA X-RAY DIFFRACTION AUTHOR J.D.ROBERTUS,L.A.MANZANO,K.R.JASHEWAY,A.F.MONZINGO,R.SAITO,J.M.PRUET, AUTHOR 2 P.A.WIGET,E.V.ANSLYN REVDAT 5 20-SEP-23 4HV3 1 REMARK SEQADV REVDAT 4 15-NOV-17 4HV3 1 REMARK REVDAT 3 29-APR-15 4HV3 1 HETSYN REVDAT 2 06-MAR-13 4HV3 1 JRNL REVDAT 1 26-DEC-12 4HV3 0 JRNL AUTH R.SAITO,J.M.PRUET,L.A.MANZANO,K.JASHEWAY,A.F.MONZINGO, JRNL AUTH 2 P.A.WIGET,I.KAMAT,E.V.ANSLYN,J.D.ROBERTUS JRNL TITL PEPTIDE-CONJUGATED PTERINS AS INHIBITORS OF RICIN TOXIN A. JRNL REF J.MED.CHEM. V. 56 320 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23214944 JRNL DOI 10.1021/JM3016393 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 46787 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2500 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3095 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2122 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -1.10000 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): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.277 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2224 ; 0.028 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3027 ; 2.806 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 267 ; 5.905 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;35.618 ;23.056 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 342 ;16.983 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;23.066 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 331 ; 0.266 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1751 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1342 ; 1.626 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2174 ; 2.657 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 882 ; 3.969 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 853 ; 6.055 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4HV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49375 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 61.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1RTC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 MALONATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 70.33650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.91350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.91350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.16825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.91350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.91350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.50475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.91350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.91350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.16825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.91350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.91350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.50475 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 70.33650 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 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 CG LEU A 151 O HOH A 576 1.50 REMARK 500 O GLN A 266 O HOH A 509 1.59 REMARK 500 NH1 ARG A 85 O HOH A 550 1.64 REMARK 500 CD2 LEU A 151 O HOH A 576 1.67 REMARK 500 CB VAL A 76 O HOH A 453 1.67 REMARK 500 O HOH A 458 O HOH A 613 1.80 REMARK 500 O HOH A 523 O HOH A 592 1.90 REMARK 500 N SER A 264 O HOH A 538 2.03 REMARK 500 O HOH A 436 O HOH A 593 2.03 REMARK 500 CB ASN A 136 O HOH A 609 2.15 REMARK 500 CG GLN A 266 O HOH A 598 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE1 PHE A 267 O HOH A 527 4444 1.86 REMARK 500 NH1 ARG A 125 OE1 GLN A 266 3455 2.10 REMARK 500 CZ PHE A 267 O4 19L A 301 4444 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 64 CA ASN A 64 CB 0.265 REMARK 500 ASN A 64 CB ASN A 64 CG -0.163 REMARK 500 ASN A 64 CG ASN A 64 OD1 0.135 REMARK 500 ASN A 64 CG ASN A 64 ND2 -0.160 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 3 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 PHE A 24 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASN A 64 C - N - CA ANGL. DEV. = 17.7 DEGREES REMARK 500 ASN A 64 CA - CB - CG ANGL. DEV. = -20.0 DEGREES REMARK 500 ASN A 64 CB - CG - OD1 ANGL. DEV. = -21.3 DEGREES REMARK 500 ASN A 64 CB - CG - ND2 ANGL. DEV. = 17.1 DEGREES REMARK 500 TYR A 84 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR A 84 CG - CD2 - CE2 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR A 84 CD1 - CE1 - CZ ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR A 91 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ILE A 104 CG1 - CB - CG2 ANGL. DEV. = 14.7 DEGREES REMARK 500 TYR A 123 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 124 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 LEU A 133 CB - CG - CD1 ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 LEU A 151 CB - CG - CD2 ANGL. DEV. = 14.0 DEGREES REMARK 500 GLU A 187 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 197 CD - NE - CZ ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 197 NE - CZ - NH2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG A 258 NE - CZ - NH1 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 258 NE - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 SER A 265 N - CA - C ANGL. DEV. = 17.0 DEGREES 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 PRO A 3 125.67 -37.28 REMARK 500 LYS A 4 -127.94 71.14 REMARK 500 GLN A 5 124.14 147.72 REMARK 500 SER A 264 14.17 122.79 REMARK 500 SER A 265 -64.87 -134.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: (2S)-2-[[(2S)-2-[(2-AZANYL-4-OXIDANYLIDENE-1H- REMARK 630 PTERIDIN-7-YL)CARBONYLAMINO]-3-OXIDANYL-PROPANOYL]AMINO]-3-(1H- REMARK 630 INDOL-3-YL)PROPANOIC ACID REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 19L A 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: JP2 SER TRP REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 19L A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLA A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RTC RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN (RECOMBINANT) REMARK 900 RELATED ID: 1IFT RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN (RECOMBINANT) REMARK 900 RELATED ID: 1BR6 RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH PTEROIC ACID REMARK 900 RELATED ID: 1PX8 RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH 7-CARBOXY-PTERIN REMARK 900 RELATED ID: 1PX9 RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH N-(FURANYLMETHYL)-7-CARBAMOYL- REMARK 900 PTERIN REMARK 900 RELATED ID: 4ESI RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH N-((1H-1,2,3-TRIAZOL-4-YL) REMARK 900 METHYL-2-AMINO-4-OXO-3,4-DIHYDROPTERIDINE-7-CARBOXAMIDE REMARK 900 RELATED ID: 4HUO RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH N-(N-(PTERIN-7-YL) REMARK 900 CARBONYLGLYCYL)-L-PHENYLALANINE REMARK 900 RELATED ID: 4HUP RELATED DB: PDB REMARK 900 STRUCTURE OF RICIN A CHAIN BOUND WITH N-(N-(N-(PTERIN-7-YL) REMARK 900 CARBONYLGLYCYL)-L-PHENYLALANYL)-L-PHENYLALANINE REMARK 900 RELATED ID: 4HV7 RELATED DB: PDB DBREF 4HV3 A 1 267 UNP P02879 RICI_RICCO 36 302 SEQADV 4HV3 MET A 0 UNP P02879 EXPRESSION TAG 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 19L A 301 35 HET SO4 A 302 5 HET MLA A 303 7 HET MLA A 304 7 HETNAM 19L (2S)-2-[[(2S)-2-[(2-AZANYL-4-OXIDANYLIDENE-1H-PTERIDIN- HETNAM 2 19L 7-YL)CARBONYLAMINO]-3-OXIDANYL-PROPANOYL]AMINO]-3-(1H- HETNAM 3 19L INDOL-3-YL)PROPANOIC ACID HETNAM SO4 SULFATE ION HETNAM MLA MALONIC ACID HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 2 19L C21 H20 N8 O6 FORMUL 3 SO4 O4 S 2- FORMUL 4 MLA 2(C3 H4 O4) FORMUL 6 HOH *221(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 SER A 155 GLY A 157 5 3 HELIX 8 8 GLN A 160 ILE A 175 1 16 HELIX 9 9 ILE A 175 PHE A 181 1 7 HELIX 10 10 PHE A 181 ASN A 195 1 15 HELIX 11 11 ASP A 201 SER A 210 1 10 HELIX 12 12 SER A 210 GLU A 220 1 11 HELIX 13 13 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 GLU A 61 N ILE A 9 SHEET 3 A 6 SER A 69 ASP A 75 -1 O LEU A 72 N VAL A 60 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 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 19 ALA A 79 TYR A 80 VAL A 81 PHE A 93 SITE 2 AC1 19 GLY A 121 ASN A 122 TYR A 123 ILE A 172 SITE 3 AC1 19 SER A 176 ARG A 180 GLU A 208 TRP A 211 SITE 4 AC1 19 ARG A 258 PHE A 267 HOH A 417 HOH A 418 SITE 5 AC1 19 HOH A 527 HOH A 553 HOH A 592 SITE 1 AC2 4 THR A 17 GLN A 19 HIS A 65 HOH A 411 SITE 1 AC3 3 ASN A 195 ARG A 197 HOH A 428 SITE 1 AC4 4 ARG A 234 PHE A 240 HOH A 534 HOH A 593 CRYST1 67.827 67.827 140.673 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 0.014743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007109 0.00000