10 20 30 40 50 60 70 80 1LLR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 30-APR-02 1LLR
TITLE CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0012
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHOLERA TOXIN B SUBUNIT; 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
KEYWDS ENTEROTOXIN, RECEPTOR, B-PENTAMER
EXPDTA X-RAY DIFFRACTION
AUTHOR E.A.MERRITT,W.G.J.HOL
REVDAT 3 24-FEB-09 1LLR 1 VERSN REVDAT 2 01-APR-03 1LLR 1 JRNL REVDAT 1 14-AUG-02 1LLR 0
JRNL AUTH E.A.MERRITT,Z.ZHANG,J.C.PICKENS,M.AHN,W.G.HOL,E.FAN JRNL TITL CHARACTERIZATION AND CRYSTAL STRUCTURE OF A JRNL TITL 2 HIGH-AFFINITY PENTAVALENT RECEPTOR-BINDING JRNL TITL 3 INHIBITOR FOR CHOLERA TOXIN AND E. COLI JRNL TITL 4 HEAT-LABILE ENTEROTOXIN. JRNL REF J.AM.CHEM.SOC. V. 124 8818 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 12137534 JRNL DOI 10.1021/JA0202560
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 4 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 84750 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : RFREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4244 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4098 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 225 REMARK 3 SOLVENT ATOMS : 570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.177 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.020 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.040 ; 0.040 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) : 0.160 ; 0.150 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) : 1.060 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.600 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.440 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PROTEIN + FNG RESIDUES REFINED WITH REMARK 3 ANISOTROPIC UIJ. REMAINDER OF LIGAND ATOMS IN MODEL REFINED REMARK 3 WITH ISOTROPIC U.
REMARK 4 REMARK 4 1LLR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB016062.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84902 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 300, NACL, MGCL2, TRIS HCL, PH REMARK 280 7.50, VAPOR DIFFUSION, SITTING DROP
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 51.19550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.98200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.19550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.98200 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: 17850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 OE1 GLN E 16 ND2 ASN E 89 2.12 REMARK 500 O HOH H 1579 O HOH H 1603 2.13 REMARK 500 CE LYS E 81 O ALA E 102 2.15 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 O HOH D 170 O HOH E 177 4445 1.87 REMARK 500 NZ LYS H 43 O HOH F 1376 4546 1.88 REMARK 500 OG SER E 55 OD1 ASP G 59 2555 2.19 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 GLU E 29 CB GLU E 29 CG -0.140 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 THR D 1 OG1 - CB - CG2 ANGL. DEV. = 16.8 DEGREES REMARK 500 THR D 1 CA - CB - OG1 ANGL. DEV. = -16.7 DEGREES REMARK 500 THR D 1 CA - CB - CG2 ANGL. DEV. = -12.9 DEGREES REMARK 500 TYR D 12 CZ - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 HIS D 13 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 HIS D 18 CE1 - NE2 - CD2 ANGL. DEV. = 8.8 DEGREES REMARK 500 ASP D 22 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG D 35 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG D 35 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG D 67 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 LYS D 81 CG - CD - CE ANGL. DEV. = 19.4 DEGREES REMARK 500 LYS D 81 CD - CE - NZ ANGL. DEV. = 29.3 DEGREES REMARK 500 HIS D 94 CE1 - NE2 - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASN D 103 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 CYS E 9 CA - CB - SG ANGL. DEV. = 10.6 DEGREES REMARK 500 TYR E 12 CB - CG - CD2 ANGL. DEV. = 3.6 DEGREES REMARK 500 TYR E 12 CB - CG - CD1 ANGL. DEV. = -7.3 DEGREES REMARK 500 GLU E 29 CA - CB - CG ANGL. DEV. = 15.9 DEGREES REMARK 500 GLU E 29 OE1 - CD - OE2 ANGL. DEV. = 12.3 DEGREES REMARK 500 GLU E 29 CG - CD - OE2 ANGL. DEV. = -12.2 DEGREES REMARK 500 ARG E 35 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG E 35 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG E 67 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 GLU E 83 OE1 - CD - OE2 ANGL. DEV. = -8.5 DEGREES REMARK 500 THR F 1 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 ASP F 7 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 GLU F 11 OE1 - CD - OE2 ANGL. DEV. = -7.2 DEGREES REMARK 500 TYR F 12 CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 LYS F 34 CB - CG - CD ANGL. DEV. = 17.2 DEGREES REMARK 500 PHE F 48 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 LYS F 62 CB - CG - CD ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG F 67 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG F 73 CD - NE - CZ ANGL. DEV. = 10.0 DEGREES REMARK 500 ALA F 102 O - C - N ANGL. DEV. = 10.2 DEGREES REMARK 500 ASP G 7 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 GLU G 11 OE1 - CD - OE2 ANGL. DEV. = -8.4 DEGREES REMARK 500 TYR G 12 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 HIS G 18 CE1 - NE2 - CD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 LYS G 34 CB - CG - CD ANGL. DEV. = 22.6 DEGREES REMARK 500 ARG G 35 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG G 67 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG G 73 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 CYS H 9 CA - CB - SG ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG H 35 NH1 - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -8.9 DEGREES REMARK 500 SER H 60 O - C - N ANGL. DEV. = -10.3 DEGREES REMARK 500 LYS H 62 CD - CE - NZ ANGL. DEV. = 22.3 DEGREES REMARK 500 ARG H 67 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 TYR H 76 CG - CD2 - CE2 ANGL. DEV. = 4.8 DEGREES REMARK 500 TYR H 76 CZ - CE2 - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. 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 GLU E 83 -71.13 -79.67 REMARK 500 ARG G 35 40.52 -140.15 REMARK 500 GLU G 83 -70.91 -80.62 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 H1154 DISTANCE = 9.86 ANGSTROMS REMARK 525 HOH H1361 DISTANCE = 10.57 ANGSTROMS REMARK 525 HOH G1456 DISTANCE = 9.32 ANGSTROMS REMARK 525 HOH G1464 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH E 210 DISTANCE = 5.57 ANGSTROMS REMARK 525 HOH H1590 DISTANCE = 5.42 ANGSTROMS
REMARK 600 REMARK 600 HETEROGEN REMARK 600 LIGAND BMS-0012 IS A PENTAVALENT LIGAND REMARK 600 CONSISTING OF A PENTACYCLEN CORE TO WHICH REMARK 600 ARE LINKED FIVE LONG ARMS, EACH CONTAINING REMARK 600 TWO 'LINKER' MOITIES AND TERMINATING IN A REMARK 600 'FINGER' DERIVED FROM METANITROPHENYLGALACTOSIDE. REMARK 600 FOR REFINEMENT THE LIGAND WAS BROKEN INTO PIECES: REMARK 600 FNG (FOR 'FINGER') IS DERIVED FROM REMARK 600 METANITROPHENYL-ALPHA-D-GALACTOPYRANOSIDE. REMARK 600 LNQ (FOR 'LINKER') IS A LINKER GROUP PRESENT IN REMARK 600 TWO COPIES PER ARM, ONLY ONE OF WHICH IS INCLUDED REMARK 600 IN THE MODEL. THERE IS AN ADDITIONAL PENTANE-2-ONE REMARK 600 WHICH LINKS THE LNQ TO THE CORE. REMARK 600 COR (FOR 'CORE', 1,4,7,10,13PENTAAZA-CYCLOPENTADECANE) REMARK 600 IS NOT PRESENT IN THIS PDB FILE BECAUSE IT WAS NOT REMARK 600 SUFFICIENTLY WELL ORDERED TO BE INCLUDED IN THE REMARK 600 STRUCTURAL MODEL. REMARK 600 THE CENTRAL CORE OF THE LIGAND IS INFERRED TO REMARK 600 LIE NEAR THE CENTRAL PORE OF THE PENTAMERIC PROTEIN. REMARK 600 REMARK 600 WATER NUMBERING RETAINED FROM 3CHB EXCEPT THAT REMARK 600 CANONICAL SITES (FORMERLY 7000) ARE GIVEN THE REMARK 600 FOLLOWING NUMBERS: REMARK 600 REMARK 600 001-009 CANONICAL WATERS AT BINDING SITE OF CHAIN D REMARK 600 101-109 CANONICAL WATERS AT BINDING SITE OF CHAIN E REMARK 600 201-209 CANONICAL WATERS AT BINDING SITE OF CHAIN F REMARK 600 301-309 CANONICAL WATERS AT BINDING SITE OF CHAIN G REMARK 600 401-409 CANONICAL WATERS AT BINDING SITE OF CHAIN H REMARK 600 REMARK 600 ALL OTHER WATERS (FORMERLY 9000) GIVEN RESIDUE REMARK 600 NUMBERS 1001-1733.
REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 LNQ D 105 REMARK 615 LNQ E 105 REMARK 615 LNQ F 105 REMARK 615 LNQ G 105 REMARK 615 LNQ H 105
REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED
REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNG D 104 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LNQ D 105 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNG E 104 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LNQ E 105 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNG F 104 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LNQ F 105 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNG G 104 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LNQ G 105 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNG H 104 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LNQ H 105
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CHB RELATED DB: PDB REMARK 900 ISOMORPHOUS COMPLEX OF CTB WITH NATIVE RECEPTOR SACCHARIDE REMARK 900 RELATED ID: 1EEI RELATED DB: PDB REMARK 900 IEE1 IS CTB COMPLEXED WITH MNPG, FROM WHICH FNG IS DERIVED
DBREF 1LLR D 1 103 GB 48890 X58785 22 124 DBREF 1LLR E 1 103 GB 48890 X58785 22 124 DBREF 1LLR F 1 103 GB 48890 X58785 22 124 DBREF 1LLR G 1 103 GB 48890 X58785 22 124 DBREF 1LLR H 1 103 GB 48890 X58785 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 FNG D 104 24 HET LNQ D 105 21 HET FNG E 104 24 HET LNQ E 105 21 HET FNG F 104 24 HET LNQ F 105 21 HET FNG G 104 24 HET LNQ G 105 21 HET FNG H 104 24 HET LNQ H 105 21
HETNAM FNG 5-AMINOCARBONYL-3-NITROPHENYL-ALPHA-D-GALACTOPYRANOSE HETNAM LNQ 3-AMINO-4-{3-[2-(2-PROPOXY-ETHOXY)-ETHOXY]- HETNAM 2 LNQ PROPYLAMINO}-CYCLOBUT-3-ENE-1,2-DIONE
FORMUL 6 FNG 5(C13 H16 N2 O9) FORMUL 6 LNQ 5(C14 H24 N2 O5) FORMUL 11 HOH *570(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 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 N VAL D 82 O ASP D 22 SHEET 3 A39 HIS D 94 ALA D 102 -1 O ALA D 95 N TRP D 88 SHEET 4 A39 THR D 47 VAL D 50 1 O THR D 47 N HIS D 94 SHEET 5 A39 MET D 37 THR D 41 -1 O ALA D 38 N VAL D 50 SHEET 6 A39 SER D 26 SER D 30 -1 O SER D 26 N THR D 41 SHEET 7 A39 HIS H 94 ALA H 102 -1 N ILE H 99 O GLU D 29 SHEET 8 A39 VAL H 82 TRP H 88 -1 N GLU H 83 O SER H 100 SHEET 9 A39 THR H 15 ASP H 22 -1 O GLN H 16 N VAL H 87 SHEET 10 A39 VAL H 82 TRP H 88 -1 N VAL H 82 O ASP H 22 SHEET 11 A39 HIS H 94 ALA H 102 -1 O ALA H 95 N TRP H 88 SHEET 12 A39 THR H 47 VAL H 50 1 O THR H 47 N HIS H 94 SHEET 13 A39 MET H 37 THR H 41 -1 O ALA H 38 N VAL H 50 SHEET 14 A39 SER H 26 SER H 30 -1 O SER H 26 N THR H 41 SHEET 15 A39 HIS G 94 ALA G 102 -1 N ILE G 99 O GLU H 29 SHEET 16 A39 VAL G 82 TRP G 88 -1 N GLU G 83 O SER G 100 SHEET 17 A39 THR G 15 ASP G 22 -1 O GLN G 16 N VAL G 87 SHEET 18 A39 VAL G 82 TRP G 88 -1 N VAL G 82 O ASP G 22 SHEET 19 A39 HIS G 94 ALA G 102 -1 O ALA G 95 N TRP G 88 SHEET 20 A39 THR G 47 VAL G 50 1 O THR G 47 N HIS G 94 SHEET 21 A39 MET G 37 THR G 41 -1 O ALA G 38 N VAL G 50 SHEET 22 A39 SER G 26 SER G 30 -1 N SER G 26 O THR G 41 SHEET 23 A39 HIS F 94 ALA F 102 -1 O ILE F 99 N GLU G 29 SHEET 24 A39 VAL F 82 TRP F 88 -1 N GLU F 83 O SER F 100 SHEET 25 A39 THR F 15 ASP F 22 -1 O GLN F 16 N VAL F 87 SHEET 26 A39 VAL F 82 TRP F 88 -1 N VAL F 82 O ASP F 22 SHEET 27 A39 HIS F 94 ALA F 102 -1 O ALA F 95 N TRP F 88 SHEET 28 A39 THR F 47 VAL F 50 1 O THR F 47 N HIS F 94 SHEET 29 A39 MET F 37 THR F 41 -1 O ALA F 38 N VAL F 50 SHEET 30 A39 SER F 26 SER F 30 -1 O SER F 26 N THR F 41 SHEET 31 A39 HIS E 94 ALA E 102 -1 N ILE E 99 O GLU F 29 SHEET 32 A39 VAL E 82 TRP E 88 -1 N GLU E 83 O SER E 100 SHEET 33 A39 THR E 15 ASP E 22 -1 O GLN E 16 N VAL E 87 SHEET 34 A39 VAL E 82 TRP E 88 -1 N VAL E 82 O ASP E 22 SHEET 35 A39 HIS E 94 ALA E 102 -1 O ALA E 95 N TRP E 88 SHEET 36 A39 THR E 47 VAL E 50 1 O THR E 47 N HIS E 94 SHEET 37 A39 ALA E 38 THR E 41 -1 O ALA E 38 N VAL E 50 SHEET 38 A39 SER E 26 SER E 30 -1 O SER E 26 N THR E 41 SHEET 39 A39 HIS D 94 ALA D 102 1 O ILE D 99 N GLU E 29
SSBOND 1 CYS D 9 CYS D 86 1555 1555 2.10 SSBOND 2 CYS E 9 CYS E 86 1555 1555 2.02 SSBOND 3 CYS F 9 CYS F 86 1555 1555 2.08 SSBOND 4 CYS G 9 CYS G 86 1555 1555 2.05 SSBOND 5 CYS H 9 CYS H 86 1555 1555 2.03
LINK N15 FNG D 104 C1 LNQ D 105 1555 1555 1.46 LINK N15 FNG E 104 C1 LNQ E 105 1555 1555 1.49 LINK N15 FNG F 104 C1 LNQ F 105 1555 1555 1.49 LINK N15 FNG G 104 C1 LNQ G 105 1555 1555 1.46 LINK N15 FNG H 104 C1 LNQ H 105 1555 1555 1.52
CISPEP 1 THR D 92 PRO D 93 0 -10.02 CISPEP 2 THR E 92 PRO E 93 0 -17.01 CISPEP 3 THR F 92 PRO F 93 0 -11.93 CISPEP 4 THR G 92 PRO G 93 0 -9.68 CISPEP 5 THR H 92 PRO H 93 0 -14.76
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 LNQ D 105 HOH D 106 HOH D 110 GLY E 33 SITE 1 AC2 6 GLU D 11 TYR D 12 HIS D 13 FNG D 104 SITE 2 AC2 6 HOH D 180 HOH D 218 SITE 1 AC3 13 TYR E 12 GLU E 51 GLN E 56 HIS E 57 SITE 2 AC3 13 GLN E 61 TRP E 88 ASN E 90 LYS E 91 SITE 3 AC3 13 LNQ E 105 HOH E 106 HOH E 109 HOH E 111 SITE 4 AC3 13 GLY F 33 SITE 1 AC4 5 GLU E 11 TYR E 12 FNG E 104 HOH E 212 SITE 2 AC4 5 LYS F 34 SITE 1 AC5 13 TYR F 12 GLU F 51 GLN F 56 HIS F 57 SITE 2 AC5 13 GLN F 61 TRP F 88 ASN F 90 LYS F 91 SITE 3 AC5 13 LNQ F 105 HOH F 201 HOH F 205 HOH F 207 SITE 4 AC5 13 GLY G 33 SITE 1 AC6 4 GLU F 11 TYR F 12 FNG F 104 HOH F1730 SITE 1 AC7 13 TYR G 12 GLU G 51 GLN G 56 HIS G 57 SITE 2 AC7 13 GLN G 61 TRP G 88 ASN G 90 LYS G 91 SITE 3 AC7 13 LNQ G 105 HOH G 301 HOH G 305 HOH G 307 SITE 4 AC7 13 GLY H 33 SITE 1 AC8 5 GLU G 11 TYR G 12 HIS G 13 FNG G 104 SITE 2 AC8 5 HOH G1731 SITE 1 AC9 13 GLY D 33 TYR H 12 GLU H 51 GLN H 56 SITE 2 AC9 13 HIS H 57 GLN H 61 TRP H 88 ASN H 90 SITE 3 AC9 13 LYS H 91 LNQ H 105 HOH H 401 HOH H 405 SITE 4 AC9 13 HOH H 407 SITE 1 BC1 4 GLU H 11 TYR H 12 FNG H 104 HOH H1732
CRYST1 102.391 65.964 78.146 90.00 105.97 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 0.009766 0.000000 0.002795 0.00000
SCALE2 0.000000 0.015160 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013310 0.00000