HEADER LECTIN 18-MAY-05 2BS7 TITLE CRYSTAL STRUCTURE OF F17B-G IN COMPLEX WITH CHITOBIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: F17BG LECTIN; COMPND 3 CHAIN: 1; COMPND 4 FRAGMENT: LECTIN 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 VARIANT: VARIANT B; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAD; SOURCE 10 OTHER_DETAILS: F17-POSITIVE ISOLATE E. COLI STRAIN KEYWDS BACTERIAL ADHESIN, BACTERIAL ATTACHMENT, PATHOGENESIS, IMMUNOGLOBULIN KEYWDS 2 FOLD ADHESIN, LECTIN, FIMBRIAE, PROTEIN-SUGAR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.BUTS,A.WELLENS,I.VAN MOLLE,L.WYNS,R.LORIS,M.LAHMANN,S.OSCARSON,H.DE AUTHOR 2 GREVE,J.BOUCKAERT REVDAT 5 29-JUL-20 2BS7 1 COMPND REMARK HET HETNAM REVDAT 5 2 1 FORMUL LINK SITE ATOM REVDAT 4 24-JUL-19 2BS7 1 REMARK REVDAT 3 08-MAY-19 2BS7 1 REMARK REVDAT 2 24-FEB-09 2BS7 1 VERSN REVDAT 1 24-MAY-06 2BS7 0 JRNL AUTH L.BUTS,A.WELLENS,I.VAN MOLLE,L.WYNS,R.LORIS,M.LAHMANN, JRNL AUTH 2 S.OSCARSON,H.DE GREVE,J.BOUCKAERT JRNL TITL IMPACT OF NATURAL VARIATION IN BACTERIAL F17G ADHESINS ON JRNL TITL 2 CRYSTALLIZATION BEHAVIOUR. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1149 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16041081 JRNL DOI 10.1107/S0907444905017038 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1204868.920 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 14326 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 SET) : 0.216 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1458 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 35.00 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1329 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.01000 REMARK 3 B22 (A**2) : 1.01000 REMARK 3 B33 (A**2) : -2.02000 REMARK 3 B12 (A**2) : 9.18000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 70.38 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BS7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1290024072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 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) : 0.8 REMARK 200 MONOCHROMATOR : TRIANGULAR MONOCHROMATOR REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8000 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1O9W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP: 1 MICROLITER OF 1.2 M REMARK 280 LI2SO4, 10 MM NICL2, 100 MM TRIS PH 8.5 PLUS 1 MICROLITER 16 MG/ REMARK 280 ML F17BG, PH 8.50, VAPOR DIFFUSION, HANGING DROP 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 38.02867 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 19.01433 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 38.02867 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 19.01433 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 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 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 SER 1 134 OG 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 SG CYS 1 53 OG SER 1 110 2.12 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 MET 1 25 30.13 76.74 REMARK 500 ALA 1 136 -19.88 69.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF F17B-G IN COMPLEX WITH N-ACETYL-D-GLUCOSAMINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THR176 NOT VISIBLE IN THE ELECTRON DENSITY DBREF 2BS7 1 1 112 UNP Q47200 Q47200_ECOLI 23 133 DBREF 2BS7 1 114 177 UNP Q47200 Q47200_ECOLI 134 198 SEQRES 1 1 176 VAL VAL SER PHE ILE GLY SER THR GLU ASN ASP VAL GLY SEQRES 2 1 176 PRO SER GLN GLY SER TYR SER SER THR HIS ALA MET ASP SEQRES 3 1 176 ASN LEU PRO PHE VAL TYR ASN THR GLY TYR ASN ILE GLY SEQRES 4 1 176 TYR GLN ASN ALA ASN VAL TRP ARG ILE GLY GLY GLY PHE SEQRES 5 1 176 CYS VAL GLY LEU ASP GLY LYS VAL ASP LEU PRO VAL VAL SEQRES 6 1 176 GLY SER LEU ASP GLY GLN SER ILE TYR GLY LEU THR GLU SEQRES 7 1 176 GLU VAL GLY LEU LEU ILE TRP MET GLY ASP THR ASN TYR SEQRES 8 1 176 SER ARG GLY THR ALA MET SER GLY ASN SER TRP GLU ASN SEQRES 9 1 176 VAL PHE SER GLY TRP SER VAL GLY ASN TYR LEU SER THR SEQRES 10 1 176 GLN GLY LEU SER VAL HIS VAL ARG PRO VAL ILE LEU LYS SEQRES 11 1 176 ARG ASN SER SER ALA GLN TYR SER VAL GLN LYS THR SER SEQRES 12 1 176 ILE GLY SER ILE ARG MET ARG PRO TYR ASN GLY SER SER SEQRES 13 1 176 ALA GLY SER VAL GLN THR THR VAL ASN PHE SER LEU ASN SEQRES 14 1 176 PRO PHE THR LEU ASN ASP THR HET NAG A 1 15 HET NAG A 2 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 HOH *116(H2 O) HELIX 1 1 ASN 1 90 GLY 1 94 5 5 SHEET 1 1A 4 VAL 1 2 PHE 1 4 0 SHEET 2 1A 4 GLY 1 39 GLY 1 49 -1 O ARG 1 47 N SER 1 3 SHEET 3 1A 4 LEU 1 116 ILE 1 129 -1 O SER 1 117 N ILE 1 48 SHEET 4 1A 4 PHE 1 30 VAL 1 31 -1 O PHE 1 30 N ILE 1 129 SHEET 1 1B 4 VAL 1 2 PHE 1 4 0 SHEET 2 1B 4 GLY 1 39 GLY 1 49 -1 O ARG 1 47 N SER 1 3 SHEET 3 1B 4 LEU 1 116 ILE 1 129 -1 O SER 1 117 N ILE 1 48 SHEET 4 1B 4 VAL 1 80 GLY 1 87 -1 O GLY 1 81 N VAL 1 128 SHEET 1 1C 5 GLU 1 9 VAL 1 12 0 SHEET 2 1C 5 THR 1 164 LEU 1 169 1 O ASN 1 166 N ASN 1 10 SHEET 3 1C 5 THR 1 143 PRO 1 152 -1 O THR 1 143 N LEU 1 169 SHEET 4 1C 5 CYS 1 53 VAL 1 60 -1 O GLY 1 55 N ARG 1 151 SHEET 5 1C 5 GLU 1 103 SER 1 110 -1 O GLU 1 103 N GLY 1 58 SHEET 1 1D 3 GLY 1 17 SER 1 21 0 SHEET 2 1D 3 PHE 1 172 ASP 1 176 1 O THR 1 173 N TYR 1 19 SHEET 3 1D 3 GLN 1 137 VAL 1 140 -1 O TYR 1 138 N LEU 1 174 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.40 CISPEP 1 LEU 1 28 PRO 1 29 0 -0.31 CRYST1 86.698 86.698 57.043 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 0.011534 0.006659 0.000000 0.00000 SCALE2 0.000000 0.013319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017531 0.00000 MASTER 267 0 2 1 16 0 0 6 0 0 0 14 END