1RDP - Header Asymmetric Unit

HEADER TOXIN 05-NOV-03 1RDP

TITLE CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT TITLE 2 NITROPHENOL-GALACTOSIDE LIGAND BV3

COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHOLERA TOXIN B PROTEIN (CTB); COMPND 3 CHAIN: D, E, F, G, H; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: CTXB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TOP10; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAD

KEYWDS BIVALENT, CHOLERA, TOXIN, PENTAMER, COMPLEX

EXPDTA X-RAY DIFFRACTION

AUTHOR J.C.PICKENS,D.D.MITCHELL,J.LIU,X.TAN,Z.ZHANG,C.L.VERLINDE, AUTHOR 2 W.G.HOL,E.FAN

REVDAT 2 24-FEB-09 1RDP 1 VERSN REVDAT 1 26-OCT-04 1RDP 0

JRNL AUTH J.C.PICKENS,D.D.MITCHELL,J.LIU,X.TAN,Z.ZHANG, JRNL AUTH 2 C.L.VERLINDE,W.G.HOL,E.FAN JRNL TITL NONSPANNING BIVALENT LIGANDS AS IMPROVED SURFACE JRNL TITL 2 RECEPTOR BINDING INHIBITORS OF THE CHOLERA TOXIN B JRNL TITL 3 PENTAMER. JRNL REF CHEM.BIOL. V. 11 1205 2004 JRNL REFN ISSN 1074-5521 JRNL PMID 15380181 JRNL DOI 10.1016/J.CHEMBIOL.2004.06.008

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 100384 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) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5029 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4743 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 242 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4093 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 140 REMARK 3 SOLVENT ATOMS : 494 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.942 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4312 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3745 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5840 ; 1.501 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8773 ; 0.867 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 511 ; 6.952 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 684 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4634 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 762 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 842 ; 0.227 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4684 ; 0.297 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2296 ; 0.085 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 669 ; 0.176 ; 0.500 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): 15 ; 0.258 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.355 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.146 ; 0.500 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): 2581 ; 2.658 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4194 ; 3.476 ; 4.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1731 ; 4.376 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1646 ; 6.083 ; 6.000 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4312 ; 2.112 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 494 ;21.699 ;15.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4233 ; 6.002 ;15.000 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS, MAXIMUM LIKELIHOOD

REMARK 4 REMARK 4 1RDP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-03. REMARK 100 THE RCSB ID CODE IS RCSB020668.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 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 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100384 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 3.660 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.22 REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: XTALVIEW REMARK 200 STARTING MODEL: PDB ENTRY 3CHB REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000, 50 MM NACL, 100 MM REMARK 280 TRIS-HCL, 20MM MGCL2, AND 2.3MM BV3, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298.0K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.04500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.03950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.04500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.03950 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F, G, H 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 O HOH F 1290 O HOH F 1389 2.02 REMARK 500 OG1 THR G 1 O HOH G 1458 2.05 REMARK 500 OD1 ASP D 59 O HOH D 1376 2.05 REMARK 500 OD2 ASP H 59 O HOH H 1385 2.08 REMARK 500 O HOH D 1174 O HOH D 1332 2.09 REMARK 500 O HOH H 1320 O HOH H 1414 2.18 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 ASP D 59 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP F 59 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG H 67 NE - CZ - NH2 ANGL. DEV. = -3.1 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 LYS D 34 -0.26 70.97 REMARK 500 GLU F 83 -70.86 -77.85 REMARK 500 REMARK 500 REMARK: NULL

REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BV3 D 104 REMARK 610 BV3 E 105 REMARK 610 BV3 F 106 REMARK 610 BV3 G 107 REMARK 610 BV3 H 108

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV3 D 104 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV3 E 105 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV3 F 106 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV3 G 107 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV3 H 108 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS H 109 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE H 110

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RCV RELATED DB: PDB REMARK 900 CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT REMARK 900 NITROPHENOL-GALACTOSIDE LIGAND BV1 REMARK 900 RELATED ID: 1RD9 RELATED DB: PDB REMARK 900 CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT REMARK 900 NITROPHENOL-GALACTOSIDE LIGAND BV2 REMARK 900 RELATED ID: 1RF2 RELATED DB: PDB REMARK 900 CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT REMARK 900 NITROPHENOL-GALACTOSIDE LIGAND BV4

DBREF 1RDP D 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RDP E 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RDP F 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RDP G 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RDP H 1 103 UNP P01556 CHTB_VIBCH 22 124

SEQRES 1 D 103 THR PRO GLN ASN ILE THR ASP LEU CYS ALA GLU TYR HIS SEQRES 2 D 103 ASN THR GLN ILE HIS THR LEU ASN ASP LYS ILE PHE SER SEQRES 3 D 103 TYR THR GLU SER LEU ALA GLY LYS ARG GLU MET ALA ILE SEQRES 4 D 103 ILE THR PHE LYS ASN GLY ALA THR PHE GLN VAL GLU VAL SEQRES 5 D 103 PRO GLY SER GLN HIS ILE ASP SER GLN LYS LYS ALA ILE SEQRES 6 D 103 GLU ARG MET LYS ASP THR LEU ARG ILE ALA TYR LEU THR SEQRES 7 D 103 GLU ALA LYS VAL GLU LYS LEU CYS VAL TRP ASN ASN LYS SEQRES 8 D 103 THR PRO HIS ALA ILE ALA ALA ILE SER MET ALA ASN SEQRES 1 E 103 THR PRO GLN ASN ILE THR ASP LEU CYS ALA GLU TYR HIS SEQRES 2 E 103 ASN THR GLN ILE HIS THR LEU ASN ASP LYS ILE PHE SER SEQRES 3 E 103 TYR THR GLU SER LEU ALA GLY LYS ARG GLU MET ALA ILE SEQRES 4 E 103 ILE THR PHE LYS ASN GLY ALA THR PHE GLN VAL GLU VAL SEQRES 5 E 103 PRO GLY SER GLN HIS ILE ASP SER GLN LYS LYS ALA ILE SEQRES 6 E 103 GLU ARG MET LYS ASP THR LEU ARG ILE ALA TYR LEU THR SEQRES 7 E 103 GLU ALA LYS VAL GLU LYS LEU CYS VAL TRP ASN ASN LYS SEQRES 8 E 103 THR PRO HIS ALA ILE ALA ALA ILE SER MET ALA ASN SEQRES 1 F 103 THR PRO GLN ASN ILE THR ASP LEU CYS ALA GLU TYR HIS SEQRES 2 F 103 ASN THR GLN ILE HIS THR LEU ASN ASP LYS ILE PHE SER SEQRES 3 F 103 TYR THR GLU SER LEU ALA GLY LYS ARG GLU MET ALA ILE SEQRES 4 F 103 ILE THR PHE LYS ASN GLY ALA THR PHE GLN VAL GLU VAL SEQRES 5 F 103 PRO GLY SER GLN HIS ILE ASP SER GLN LYS LYS ALA ILE SEQRES 6 F 103 GLU ARG MET LYS ASP THR LEU ARG ILE ALA TYR LEU THR SEQRES 7 F 103 GLU ALA LYS VAL GLU LYS LEU CYS VAL TRP ASN ASN LYS SEQRES 8 F 103 THR PRO HIS ALA ILE ALA ALA ILE SER MET ALA ASN SEQRES 1 G 103 THR PRO GLN ASN ILE THR ASP LEU CYS ALA GLU TYR HIS SEQRES 2 G 103 ASN THR GLN ILE HIS THR LEU ASN ASP LYS ILE PHE SER SEQRES 3 G 103 TYR THR GLU SER LEU ALA GLY LYS ARG GLU MET ALA ILE SEQRES 4 G 103 ILE THR PHE LYS ASN GLY ALA THR PHE GLN VAL GLU VAL SEQRES 5 G 103 PRO GLY SER GLN HIS ILE ASP SER GLN LYS LYS ALA ILE SEQRES 6 G 103 GLU ARG MET LYS ASP THR LEU ARG ILE ALA TYR LEU THR SEQRES 7 G 103 GLU ALA LYS VAL GLU LYS LEU CYS VAL TRP ASN ASN LYS SEQRES 8 G 103 THR PRO HIS ALA ILE ALA ALA ILE SER MET ALA ASN SEQRES 1 H 103 THR PRO GLN ASN ILE THR ASP LEU CYS ALA GLU TYR HIS SEQRES 2 H 103 ASN THR GLN ILE HIS THR LEU ASN ASP LYS ILE PHE SER SEQRES 3 H 103 TYR THR GLU SER LEU ALA GLY LYS ARG GLU MET ALA ILE SEQRES 4 H 103 ILE THR PHE LYS ASN GLY ALA THR PHE GLN VAL GLU VAL SEQRES 5 H 103 PRO GLY SER GLN HIS ILE ASP SER GLN LYS LYS ALA ILE SEQRES 6 H 103 GLU ARG MET LYS ASP THR LEU ARG ILE ALA TYR LEU THR SEQRES 7 H 103 GLU ALA LYS VAL GLU LYS LEU CYS VAL TRP ASN ASN LYS SEQRES 8 H 103 THR PRO HIS ALA ILE ALA ALA ILE SER MET ALA ASN

HET BV3 D 104 24 HET BV3 E 105 24 HET BV3 F 106 24 HET BV3 G 107 24 HET BV3 H 108 24 HET TRS H 109 8 HET PGE H 110 12

HETNAM BV3 1,3-BIS-([[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)- HETNAM 2 BV3 BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4- HETNAM 3 BV3 DIOXO-CYCLOBUTENYL]-AMINO-ETHYL]-AMINO-CARBONYLOXY)-2- HETNAM 4 BV3 AMINO-PROPANE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM PGE TRIETHYLENE GLYCOL

HETSYN BV3 BV3 HETSYN TRS TRIS BUFFER

FORMUL 6 BV3 5(C63 H91 N15 O26) FORMUL 11 TRS C4 H12 N O3 1+ FORMUL 12 PGE C6 H14 O4 FORMUL 13 HOH *494(H2 O)

HELIX 1 1 ASN D 4 ALA D 10 1 7 HELIX 2 2 ILE D 58 GLU D 79 1 22 HELIX 3 3 ASN E 4 ALA E 10 1 7 HELIX 4 4 SER E 60 GLU E 79 1 20 HELIX 5 5 ASN F 4 ALA F 10 1 7 HELIX 6 6 SER F 60 GLU F 79 1 20 HELIX 7 7 ASN G 4 ALA G 10 1 7 HELIX 8 8 SER G 60 GLU G 79 1 20 HELIX 9 9 ASN H 4 GLU H 11 1 8 HELIX 10 10 SER H 60 GLU H 79 1 20

SHEET 1 A39 THR D 15 ASP D 22 0 SHEET 2 A39 VAL D 82 TRP D 88 -1 O LEU D 85 N HIS D 18 SHEET 3 A39 HIS D 94 ALA D 102 -1 O ALA D 97 N CYS D 86 SHEET 4 A39 SER E 26 SER E 30 -1 O GLU E 29 N ILE D 99 SHEET 5 A39 ALA E 38 THR E 41 -1 O ILE E 39 N THR E 28 SHEET 6 A39 THR E 47 VAL E 50 -1 O PHE E 48 N ILE E 40 SHEET 7 A39 HIS E 94 ALA E 102 1 O ILE E 96 N GLN E 49 SHEET 8 A39 VAL E 82 TRP E 88 -1 N CYS E 86 O ALA E 97 SHEET 9 A39 THR E 15 ASP E 22 -1 N HIS E 18 O LEU E 85 SHEET 10 A39 VAL E 82 TRP E 88 -1 O LEU E 85 N HIS E 18 SHEET 11 A39 HIS E 94 ALA E 102 -1 O ALA E 97 N CYS E 86 SHEET 12 A39 SER F 26 SER F 30 -1 O GLU F 29 N ILE E 99 SHEET 13 A39 ALA F 38 THR F 41 -1 O ILE F 39 N THR F 28 SHEET 14 A39 THR F 47 VAL F 50 -1 O PHE F 48 N ILE F 40 SHEET 15 A39 HIS F 94 ALA F 102 1 O ILE F 96 N GLN F 49 SHEET 16 A39 LYS F 81 TRP F 88 -1 N CYS F 86 O ALA F 97 SHEET 17 A39 THR F 15 LYS F 23 -1 N GLN F 16 O VAL F 87 SHEET 18 A39 LYS F 81 TRP F 88 -1 O VAL F 87 N GLN F 16 SHEET 19 A39 HIS F 94 ALA F 102 -1 O ALA F 97 N CYS F 86 SHEET 20 A39 SER G 26 SER G 30 -1 O TYR G 27 N MET F 101 SHEET 21 A39 MET G 37 THR G 41 -1 O ILE G 39 N THR G 28 SHEET 22 A39 THR G 47 VAL G 50 -1 O PHE G 48 N ILE G 40 SHEET 23 A39 HIS G 94 ALA G 102 1 O ILE G 96 N GLN G 49 SHEET 24 A39 VAL G 82 TRP G 88 -1 N CYS G 86 O ALA G 97 SHEET 25 A39 THR G 15 ASP G 22 -1 N HIS G 18 O LEU G 85 SHEET 26 A39 VAL G 82 TRP G 88 -1 O LEU G 85 N HIS G 18 SHEET 27 A39 HIS G 94 ALA G 102 -1 O ALA G 97 N CYS G 86 SHEET 28 A39 SER H 26 SER H 30 -1 O GLU H 29 N ILE G 99 SHEET 29 A39 MET H 37 THR H 41 -1 O ILE H 39 N THR H 28 SHEET 30 A39 THR H 47 VAL H 50 -1 O PHE H 48 N ILE H 40 SHEET 31 A39 HIS H 94 ALA H 102 1 O ILE H 96 N GLN H 49 SHEET 32 A39 VAL H 82 TRP H 88 -1 N CYS H 86 O ALA H 97 SHEET 33 A39 THR H 15 ASP H 22 -1 N HIS H 18 O LEU H 85 SHEET 34 A39 VAL H 82 TRP H 88 -1 O LEU H 85 N HIS H 18 SHEET 35 A39 HIS H 94 ALA H 102 -1 O ALA H 97 N CYS H 86 SHEET 36 A39 SER D 26 SER D 30 -1 N TYR D 27 O MET H 101 SHEET 37 A39 ALA D 38 THR D 41 -1 O ILE D 39 N THR D 28 SHEET 38 A39 THR D 47 VAL D 50 -1 O PHE D 48 N ILE D 40 SHEET 39 A39 HIS D 94 ALA D 102 1 O ILE D 96 N GLN D 49

SSBOND 1 CYS D 9 CYS D 86 1555 1555 2.06 SSBOND 2 CYS E 9 CYS E 86 1555 1555 2.05 SSBOND 3 CYS F 9 CYS F 86 1555 1555 2.04 SSBOND 4 CYS G 9 CYS G 86 1555 1555 2.04 SSBOND 5 CYS H 9 CYS H 86 1555 1555 2.06

CISPEP 1 THR D 92 PRO D 93 0 -8.18 CISPEP 2 THR E 92 PRO E 93 0 -7.90 CISPEP 3 THR F 92 PRO F 93 0 -9.84 CISPEP 4 THR G 92 PRO G 93 0 -10.75 CISPEP 5 THR H 92 PRO H 93 0 -10.86

SITE 1 AC1 10 TYR D 12 GLU D 51 GLN D 56 HIS D 57 SITE 2 AC1 10 GLN D 61 TRP D 88 ASN D 90 LYS D 91 SITE 3 AC1 10 HOH D1423 GLY E 33 SITE 1 AC2 10 TYR E 12 GLU E 51 GLN E 56 HIS E 57 SITE 2 AC2 10 GLN E 61 TRP E 88 ASN E 90 LYS E 91 SITE 3 AC2 10 HOH E1419 GLY F 33 SITE 1 AC3 11 TYR F 12 GLU F 51 GLN F 56 HIS F 57 SITE 2 AC3 11 GLN F 61 TRP F 88 ASN F 90 LYS F 91 SITE 3 AC3 11 HOH F1400 HOH F1404 GLY G 33 SITE 1 AC4 12 TYR G 12 GLU G 51 GLN G 56 HIS G 57 SITE 2 AC4 12 GLN G 61 TRP G 88 ASN G 90 LYS G 91 SITE 3 AC4 12 HOH G1395 HOH G1396 HOH G1397 GLY H 33 SITE 1 AC5 11 GLY D 33 HOH E1415 TYR H 12 GLU H 51 SITE 2 AC5 11 GLN H 56 GLN H 61 TRP H 88 ASN H 90 SITE 3 AC5 11 LYS H 91 HOH H1406 HOH H1407 SITE 1 AC6 10 ARG D 35 ASN F 14 ASN F 89 ASN F 90 SITE 2 AC6 10 THR H 1 PRO H 2 ASP H 7 GLU H 11 SITE 3 AC6 10 HOH H1444 HOH H1447 SITE 1 AC7 8 LYS D 91 THR D 92 ASN F 89 ASN F 90 SITE 2 AC7 8 LYS F 91 THR F 92 THR H 1 HOH H1284

CRYST1 102.090 66.079 78.715 90.00 105.83 90.00 C 1 2 1 20

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 0.009795 0.000000 0.002778 0.00000

SCALE2 0.000000 0.015133 0.000000 0.00000

SCALE3 0.000000 0.000000 0.013205 0.00000