HEADER TOXIN 17-DEC-96 4ULL TITLE SOLUTION NMR STRUCTURE OF VEROTOXIN-1 B-SUBUNIT FROM E. COLI, 5 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHIGA TOXIN 1B; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS TOXIN EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR J.M.RICHARDSON,P.D.EVANS,S.W.HOMANS,A.DONOHUE-ROLFE REVDAT 3 11-DEC-19 4ULL 1 COMPND SOURCE REMARK DBREF REVDAT 2 24-FEB-09 4ULL 1 VERSN REVDAT 1 01-APR-97 4ULL 0 JRNL AUTH J.M.RICHARDSON,P.D.EVANS,S.W.HOMANS,A.DONOHUE-ROLFE JRNL TITL SOLUTION STRUCTURE OF THE CARBOHYDRATE-BINDING B-SUBUNIT JRNL TITL 2 HOMOPENTAMER OF VEROTOXIN VT-1 FROM E. COLI. JRNL REF NAT.STRUCT.BIOL. V. 4 190 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9164458 JRNL DOI 10.1038/NSB0397-190 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ULL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000179445. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : ASSIGNMENT HNCO; HCACO; HNCOCA; REMARK 210 3D TOCSY. 1H-1H DISTANCE REMARK 210 DERIVATION; 3D-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500.3 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING/ MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO RESTRAINT VIOLATIONS ABOVE REMARK 210 0.7 ANGSTROM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED BY TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON UNIFORMLY 13C, 15N-LABELED VEROTOXIN-1. IONIC_ REMARK 210 STRENGTH: 200 MM PRESSURE: ATMOSPHERIC SOLVENT SYSTEM: H20 REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 HZ3 LYS A 13 OG1 THR A 21 1.30 REMARK 500 OG1 THR A 6 HZ1 LYS A 8 1.31 REMARK 500 HZ2 LYS A 13 OD1 ASN A 15 1.36 REMARK 500 O ASP A 26 HZ1 LYS A 27 1.37 REMARK 500 HZ3 LYS A 53 OE1 GLU A 65 1.41 REMARK 500 OD1 ASP A 3 HZ1 LYS A 53 1.42 REMARK 500 O SER A 38 HG SER A 42 1.43 REMARK 500 O GLU A 10 HZ3 LYS A 23 1.44 REMARK 500 O LYS A 53 HG1 THR A 54 1.45 REMARK 500 HZ2 LYS A 8 O GLY A 25 1.46 REMARK 500 O ALA A 43 H GLY A 47 1.47 REMARK 500 O SER A 42 HG1 THR A 46 1.52 REMARK 500 HG1 THR A 6 OD2 ASP A 26 1.52 REMARK 500 HE ARG A 33 OG SER A 64 1.52 REMARK 500 HG1 THR A 1 OD2 ASP A 3 1.60 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 1 ASP A 3 -146.98 -88.02 REMARK 500 1 CYS A 4 -86.86 -171.42 REMARK 500 1 LYS A 8 -146.30 -72.69 REMARK 500 1 VAL A 9 66.71 -158.04 REMARK 500 1 GLU A 10 59.13 -101.29 REMARK 500 1 TYR A 11 103.80 124.05 REMARK 500 1 ASN A 15 -40.70 -165.85 REMARK 500 1 ASP A 17 -41.41 171.54 REMARK 500 1 ASP A 18 -36.64 -145.70 REMARK 500 1 THR A 19 -78.18 -48.93 REMARK 500 1 PHE A 20 176.28 69.74 REMARK 500 1 LYS A 23 72.04 -109.13 REMARK 500 1 ARG A 33 -55.15 -161.69 REMARK 500 1 TRP A 34 -26.65 178.28 REMARK 500 1 ASN A 35 69.16 179.53 REMARK 500 1 MET A 48 60.37 142.20 REMARK 500 1 THR A 49 67.55 -176.90 REMARK 500 1 VAL A 50 -151.15 -77.52 REMARK 500 1 THR A 54 161.74 67.76 REMARK 500 1 ALA A 56 -57.08 75.07 REMARK 500 1 ASN A 59 81.94 58.03 REMARK 500 1 PHE A 63 -82.75 -98.07 REMARK 500 2 ASP A 3 -146.97 -88.47 REMARK 500 2 CYS A 4 -86.45 -171.63 REMARK 500 2 LYS A 8 -145.67 -72.83 REMARK 500 2 VAL A 9 67.08 -158.23 REMARK 500 2 GLU A 10 58.12 -101.48 REMARK 500 2 TYR A 11 103.98 125.27 REMARK 500 2 ASN A 15 -40.22 -166.62 REMARK 500 2 ASP A 17 -41.04 171.22 REMARK 500 2 ASP A 18 -37.04 -145.96 REMARK 500 2 THR A 19 -78.29 -48.48 REMARK 500 2 PHE A 20 176.39 69.77 REMARK 500 2 LYS A 23 72.91 -108.42 REMARK 500 2 ARG A 33 -55.29 -161.79 REMARK 500 2 TRP A 34 -25.86 178.09 REMARK 500 2 ASN A 35 68.34 178.58 REMARK 500 2 MET A 48 60.24 141.93 REMARK 500 2 THR A 49 67.01 -177.00 REMARK 500 2 VAL A 50 -151.93 -77.57 REMARK 500 2 THR A 54 161.74 67.70 REMARK 500 2 ALA A 56 -56.92 75.16 REMARK 500 2 ASN A 59 81.81 58.13 REMARK 500 2 PHE A 63 -82.02 -97.94 REMARK 500 3 ASP A 3 -147.66 -88.10 REMARK 500 3 CYS A 4 -86.64 -170.77 REMARK 500 3 LYS A 8 -145.92 -72.84 REMARK 500 3 VAL A 9 67.19 -158.17 REMARK 500 3 GLU A 10 58.55 -101.21 REMARK 500 3 TYR A 11 103.36 124.88 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 69 0.25 SIDE CHAIN REMARK 500 2 ARG A 69 0.25 SIDE CHAIN REMARK 500 3 ARG A 69 0.25 SIDE CHAIN REMARK 500 4 ARG A 69 0.25 SIDE CHAIN REMARK 500 5 ARG A 69 0.25 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 4ULL A 1 69 UNP Q8G8Y6 Q8G8Y6_ECOLX 17 85 SEQRES 1 A 69 THR PRO ASP CYS VAL THR GLY LYS VAL GLU TYR THR LYS SEQRES 2 A 69 TYR ASN ASP ASP ASP THR PHE THR VAL LYS VAL GLY ASP SEQRES 3 A 69 LYS GLU LEU PHE THR ASN ARG TRP ASN LEU GLN SER LEU SEQRES 4 A 69 LEU LEU SER ALA GLN ILE THR GLY MET THR VAL THR ILE SEQRES 5 A 69 LYS THR ASN ALA CYS HIS ASN GLY GLY GLY PHE SER GLU SEQRES 6 A 69 VAL ILE PHE ARG HELIX 1 1 LEU A 36 THR A 46 1 11 SHEET 1 A 3 VAL A 5 GLY A 7 0 SHEET 2 A 3 VAL A 50 LYS A 53 -1 N ILE A 52 O VAL A 5 SHEET 3 A 3 GLU A 65 ILE A 67 -1 N ILE A 67 O THR A 51 SHEET 1 B 2 THR A 21 VAL A 24 0 SHEET 2 B 2 LYS A 27 PHE A 30 -1 N LEU A 29 O VAL A 22 SSBOND 1 CYS A 4 CYS A 57 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1