10 20 30 40 50 60 70 80 1RF2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 07-NOV-03 1RF2
TITLE CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT TITLE 2 NITROPHENOL-GALACTOSIDE LIGAND BV4
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 1RF2 1 VERSN REVDAT 1 26-OCT-04 1RF2 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) : 49.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 104314 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) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5219 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) : 1.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5046 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 260 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4074 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 138 REMARK 3 SOLVENT ATOMS : 498 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.04000 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): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.934 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4290 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3717 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5808 ; 1.417 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8706 ; 0.862 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ; 6.954 ; 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): 677 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4624 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 760 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 802 ; 0.220 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4668 ; 0.298 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2229 ; 0.086 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 610 ; 0.160 ; 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): 16 ; 0.230 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 39 ; 0.348 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.265 ; 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): 2576 ; 2.485 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4178 ; 3.398 ; 4.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1714 ; 5.237 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1630 ; 7.194 ; 8.000 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4290 ; 2.121 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 498 ;21.151 ;15.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4212 ; 6.669 ;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 1RF2 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 RCSB020689.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-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) : 0.9626 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 : 104314 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 (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 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 (%) : 69.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.59100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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 (%): 44.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 8000, 50 MM NACL, 100 MM REMARK 280 TRIS-HCL, 20MM MGCL2, AND 2.3MM BV4, 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 51.11750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.01400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.11750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.01400 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: 15730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 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 F1321 LIES ON A SPECIAL POSITION.
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 1211 O HOH F 1320 2.13 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. = 5.9 DEGREES REMARK 500 ARG H 73 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH E1310 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH D1373 DISTANCE = 5.65 ANGSTROMS REMARK 525 HOH E1407 DISTANCE = 6.22 ANGSTROMS
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 BV4 D 104 REMARK 610 BV4 E 105 REMARK 610 BV4 F 106 REMARK 610 BV4 G 107 REMARK 610 BV4 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 BV4 D 104 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV4 E 105 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV4 F 106 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV4 G 107 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BV4 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: 1RDP RELATED DB: PDB REMARK 900 CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT REMARK 900 NITROPHENOL-GALACTOSIDE LIGAND BV3
DBREF 1RF2 D 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RF2 E 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RF2 F 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RF2 G 1 103 UNP P01556 CHTB_VIBCH 22 124 DBREF 1RF2 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 BV4 D 104 24 HET BV4 E 105 24 HET BV4 F 106 24 HET BV4 G 107 24 HET BV4 H 108 24 HET TRS H 109 8 HET PGE H 110 10
HETNAM BV4 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5- HETNAM 2 BV4 (GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN- HETNAM 3 BV4 1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBUTENYL]-AMINO- HETNAM 4 BV4 PROPOXY-ETHOXY-ETHOXY]-PROPYL-]AMINO-CARBONYLOXY)-2- HETNAM 5 BV4 AMINO-PROPANE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM PGE TRIETHYLENE GLYCOL
HETSYN BV4 BV4 HETSYN TRS TRIS BUFFER
FORMUL 6 BV4 5(C79 H123 N15 O32) FORMUL 11 TRS C4 H12 N O3 1+ FORMUL 12 PGE C6 H14 O4 FORMUL 13 HOH *498(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 GLU F 11 1 8 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 ALA H 10 1 7 HELIX 10 10 SER H 60 GLU H 79 1 20
SHEET 1 A39 THR D 15 LYS D 23 0 SHEET 2 A39 LYS D 81 TRP D 88 -1 O VAL D 87 N GLN D 16 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 TYR E 27 N MET D 101 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 VAL F 82 TRP F 88 -1 N CYS F 86 O ALA F 97 SHEET 17 A39 THR F 15 ASP F 22 -1 N ASP F 22 O VAL F 82 SHEET 18 A39 VAL F 82 TRP F 88 -1 O VAL F 82 N ASP F 22 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 TYR H 27 N MET G 101 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 2.04 SSBOND 2 CYS E 9 CYS E 86 1555 1555 2.03 SSBOND 3 CYS F 9 CYS F 86 1555 1555 2.06 SSBOND 4 CYS G 9 CYS G 86 1555 1555 2.06 SSBOND 5 CYS H 9 CYS H 86 1555 1555 2.07
CISPEP 1 THR D 92 PRO D 93 0 -9.10 CISPEP 2 THR E 92 PRO E 93 0 -7.63 CISPEP 3 THR F 92 PRO F 93 0 -8.80 CISPEP 4 THR G 92 PRO G 93 0 -11.14 CISPEP 5 THR H 92 PRO H 93 0 -10.53
SITE 1 AC1 12 TYR D 12 GLU D 51 GLN D 56 HIS D 57 SITE 2 AC1 12 GLN D 61 TRP D 88 ASN D 90 LYS D 91 SITE 3 AC1 12 HOH D1133 HOH D1352 HOH D1481 GLY E 33 SITE 1 AC2 10 TYR E 12 GLU E 51 GLN E 56 GLN E 61 SITE 2 AC2 10 TRP E 88 ASN E 90 LYS E 91 HOH E1262 SITE 3 AC2 10 HOH E1480 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 F1049 HOH F1152 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 G1018 HOH G1137 HOH G1261 GLY H 33 SITE 1 AC5 13 GLY D 33 TYR H 12 GLU H 51 GLN H 56 SITE 2 AC5 13 HIS H 57 GLN H 61 TRP H 88 ASN H 90 SITE 3 AC5 13 LYS H 91 HOH H1048 HOH H1150 HOH H1346 SITE 4 AC5 13 HOH H1479 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 H1075 HOH H1496 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 H1472
CRYST1 102.235 66.028 78.642 90.00 105.80 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 0.009781 0.000000 0.002768 0.00000
SCALE2 0.000000 0.015145 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013215 0.00000