HEADER SUGAR BINDING PROTEIN 04-DEC-08 3FFO TITLE F17B-G LECTIN DOMAIN WITH BOUND GLCNAC(BETA1-2)MAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADHESIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE-BINDING DOMAIN, RESIDUES 23-198; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: F17B-G; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-AI; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: CUSTOM (T7 PROMOTOR); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHD52 KEYWDS BACTERIAL ADHESIN, LECTIN, BACTERIAL ATTACHMENT, PATHOGENESIS, KEYWDS 2 IMMUNOGLOBULIN FOLD, CELL PROJECTION, FIMBRIUM, SUGAR BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.BUTS,A.DE BOER,J.D.M.OLSSON,W.JONCKHEERE,M.DE KERPEL,E.DE GENST, AUTHOR 2 Y.GUERARDEL,R.WILLAERT,L.WYNS,M.WUHRER,S.OSCARSON,H.DE GREVE, AUTHOR 3 J.BOUCKAERT REVDAT 6 01-NOV-23 3FFO 1 HETSYN REVDAT 5 29-JUL-20 3FFO 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 17-DEC-14 3FFO 1 HETATM JRNL LINK REVDAT 3 28-AUG-13 3FFO 1 JRNL HET HETATM HETNAM REVDAT 2 13-JUL-11 3FFO 1 VERSN REVDAT 1 22-DEC-09 3FFO 0 JRNL AUTH E.LONARDI,K.MOONENS,L.BUTS,A.R.DE BOER,J.D.M.OLSSON, JRNL AUTH 2 M.S.WEISS,E.FABRE,Y.GUERARDEL,A.M.DEELDER,S.OSCARSON, JRNL AUTH 3 M.WUHRER,J.BOUCKAERT JRNL TITL STRUCTURAL SAMPLING OF GLYCAN INTERACTION PROFILES REVEALS JRNL TITL 2 MUCOSAL RECEPTORS FOR FIMBRIAL ADHESINS OF ENTEROTOXIGENIC JRNL TITL 3 ESCHERICHIA COLI. JRNL REF BIOLOGY (BASEL) V. 2 894 2013 JRNL REFN ESSN 2079-7737 JRNL PMID 24833052 JRNL DOI 10.3390/BIOLOGY2030894 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14511 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1474 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 18.9210 - 4.6490 1.00 1243 123 0.1780 0.1790 REMARK 3 2 4.6490 - 3.6990 1.00 1175 155 0.1840 0.2120 REMARK 3 3 3.6990 - 3.2340 1.00 1203 117 0.2210 0.2620 REMARK 3 4 3.2340 - 2.9400 1.00 1193 126 0.2640 0.3390 REMARK 3 5 2.9400 - 2.7300 1.00 1185 131 0.2820 0.3340 REMARK 3 6 2.7300 - 2.5690 1.00 1147 166 0.3010 0.3730 REMARK 3 7 2.5690 - 2.4410 1.00 1180 135 0.3100 0.3700 REMARK 3 8 2.4410 - 2.3350 1.00 1166 139 0.3040 0.3850 REMARK 3 9 2.3350 - 2.2450 1.00 1168 142 0.3030 0.3890 REMARK 3 10 2.2450 - 2.1680 1.00 1201 117 0.2780 0.3670 REMARK 3 11 2.1680 - 2.1000 0.99 1176 123 0.2790 0.3060 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 50.71 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.08200 REMARK 3 B22 (A**2) : 3.08200 REMARK 3 B33 (A**2) : -6.16300 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1388 REMARK 3 ANGLE : 0.970 1889 REMARK 3 CHIRALITY : 0.059 211 REMARK 3 PLANARITY : 0.003 241 REMARK 3 DIHEDRAL : 18.309 479 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3FFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8453 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14544 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1O9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M LITHIUM SULPHATE, 10MM NICKEL REMARK 280 CHLORIDE, 100MM TRIS, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.87267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.93633 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.87267 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.93633 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, B 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 NI NI A 263 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 114 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 115 CG CD1 CD2 REMARK 470 SER A 133 OG REMARK 470 GLN A 140 CD OE1 NE2 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 ILE A 5 12.50 -140.92 REMARK 500 MET A 25 44.15 -70.25 REMARK 500 ASN A 113 43.44 -88.25 REMARK 500 SER A 155 154.77 -49.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1O9Z RELATED DB: PDB REMARK 900 RELATED APOPROTEIN DBREF 3FFO A 1 176 UNP Q47200 Q47200_ECOLX 23 198 SEQRES 1 A 176 VAL VAL SER PHE ILE GLY SER THR GLU ASN ASP VAL GLY SEQRES 2 A 176 PRO SER GLN GLY SER TYR SER SER THR HIS ALA MET ASP SEQRES 3 A 176 ASN LEU PRO PHE VAL TYR ASN THR GLY TYR ASN ILE GLY SEQRES 4 A 176 TYR GLN ASN ALA ASN VAL TRP ARG ILE GLY GLY GLY PHE SEQRES 5 A 176 CYS VAL GLY LEU ASP GLY LYS VAL ASP LEU PRO VAL VAL SEQRES 6 A 176 GLY SER LEU ASP GLY GLN SER ILE TYR GLY LEU THR GLU SEQRES 7 A 176 GLU VAL GLY LEU LEU ILE TRP MET GLY ASP THR ASN TYR SEQRES 8 A 176 SER ARG GLY THR ALA MET SER GLY ASN SER TRP GLU ASN SEQRES 9 A 176 VAL PHE SER GLY TRP CYS VAL GLY ASN TYR LEU SER THR SEQRES 10 A 176 GLN GLY LEU SER VAL HIS VAL ARG PRO VAL ILE LEU LYS SEQRES 11 A 176 ARG ASN SER SER ALA GLN TYR SER VAL GLN LYS THR SER SEQRES 12 A 176 ILE GLY SER ILE ARG MET ARG PRO TYR ASN GLY SER SER SEQRES 13 A 176 ALA GLY SER VAL GLN THR THR VAL ASN PHE SER LEU ASN SEQRES 14 A 176 PRO PHE THR LEU ASN ASP THR HET BMA B 1 12 HET NAG B 2 14 HET NI A 263 1 HET TRS A 207 8 HET SO4 A 205 5 HET SO4 A 206 5 HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NI NICKEL (II) ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM SO4 SULFATE ION HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN TRS TRIS BUFFER FORMUL 2 BMA C6 H12 O6 FORMUL 2 NAG C8 H15 N O6 FORMUL 3 NI NI 2+ FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *47(H2 O) HELIX 1 1 ASN A 90 GLY A 94 5 5 SHEET 1 A 6 VAL A 2 PHE A 4 0 SHEET 2 A 6 GLY A 39 GLY A 49 -1 O ARG A 47 N SER A 3 SHEET 3 A 6 LEU A 115 ILE A 128 -1 O SER A 116 N ILE A 48 SHEET 4 A 6 VAL A 80 GLY A 87 -1 N GLY A 81 O VAL A 127 SHEET 5 A 6 GLN A 71 GLY A 75 -1 N TYR A 74 O LEU A 82 SHEET 6 A 6 VAL A 64 LEU A 68 -1 N VAL A 65 O ILE A 73 SHEET 1 B 4 PHE A 30 VAL A 31 0 SHEET 2 B 4 LEU A 115 ILE A 128 -1 O ILE A 128 N PHE A 30 SHEET 3 B 4 VAL A 80 GLY A 87 -1 N GLY A 81 O VAL A 127 SHEET 4 B 4 THR A 95 ALA A 96 -1 O THR A 95 N MET A 86 SHEET 1 C 5 GLU A 9 VAL A 12 0 SHEET 2 C 5 THR A 163 LEU A 168 1 O SER A 167 N VAL A 12 SHEET 3 C 5 THR A 142 PRO A 151 -1 N THR A 142 O LEU A 168 SHEET 4 C 5 CYS A 53 VAL A 60 -1 N GLY A 55 O ARG A 150 SHEET 5 C 5 GLU A 103 CYS A 110 -1 O GLU A 103 N GLY A 58 SHEET 1 D 3 GLY A 17 SER A 21 0 SHEET 2 D 3 PHE A 171 ASP A 175 1 O ASN A 174 N TYR A 19 SHEET 3 D 3 GLN A 136 VAL A 139 -1 N TYR A 137 O LEU A 173 SSBOND 1 CYS A 53 CYS A 110 1555 1555 2.03 LINK O2 BMA B 1 C1 NAG B 2 1555 1555 1.42 CISPEP 1 LEU A 28 PRO A 29 0 3.84 CRYST1 87.389 87.389 56.809 90.00 90.00 120.00 P 62 6 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 0.011443 0.006607 0.000000 0.00000 SCALE2 0.000000 0.013213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017603 0.00000